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Here is the updated wiring diagram for your Air Handler Unit for zone 6 (AHU 6). I have added some features to the diagram to include:

1. The L6006C strap on aquastat to keep the fan from blowing cold air on start up. the fan will not operate unless
   1. The Fan Relay os in the Automatic or off position (thermostat set to Fan Auto)
   2. The Heat relay is on (thermostat calling for heat)
   3. And the coil temperature is at least 120°F (setting adjustable)
2. The ability to use two speeds on the Fan motor. By routing the heat relay through the NC contacts there will be no problem with using a different speed on the fan motor for heat and a different speed for cool or Fan On.
3. Changed the Heat relay colors to use the Prp and Brn to activate the Taco SR501.

These three changes will be a better design for future use by others in the event that someone decides that you may have a more efficient operation with a different fan speed on the blower fan motor or cool only but the leave the heat at the existing speed (or vice versa).

Note: AHU 6 and the outdoor condensing unit CU 6 may be fed 220VAC from separate circuit breakers. Make a note of what circuit breakers feed each unit on this diagram for future reference

I recommend this diagram be followed to ensure proper operation of the heat and cooling system. After completing this project and testing this system for proper operation, post this wiring diagram near the AHU 6 appliance and a second copy near the boilers. A third copy can be kept on file with other important papers.

PS. I know that we are using the L6006C Strap On aquastat is on the line voltage side of the system. This is for a good reason. If you try to use the low voltage side of the system to control that fan speed, you will end up with a "Catch 22". You need the aquastat to turn on the 24 VAC relay to heat the water, but the boiler needs the hot water to satisfy the aquastat. That is why you can't use the low voltage wires at the relay. The Heat Relay still powers the Taco SR501 but the fan won't operate until the water in the coil is hot.

Yes, you can use the Prp and Brn as the low voltage.

I was concerned with the double wires on the Taco SR501 at the 5 and 6NO connections. You should only have one set of R and W wires there that go to the boiler.

Someone should really do what @EBEBRATT-Ed mentioned earlier. You need to have a master wiring diagram of the entire system from each thermostat to the zone controls to the AHU units to the Switching Relays to the boiler controls. Then when something dies not work, you can refer to the proper wiring diagram to see how they interact with each other. Saves time when someone is trouble shooting.

You don't know how many times my mechanics went to no heat calls to be baffled by some system like yours only to find that is was something simple like a fuse on the Power Vent system. They didn't even know there was a power vent system to begin with. When I get there to help them, (and also train them on the job) I find the power vent is not allowing the gas valve/ignition control to open and light the flame. the mechanic looking for 90 minutes with no luck. (I did that in the past) …only to find the problem in five minutes once I pointed to the power vent system.

I can help with that. Send me a PM message if you are interested.

@loamyroots11 said: I'm a little confused on the NO connections though. I understand that I'm connecting the NO (Org) to the fan (just like how my current RIB relay is for heat).

I'm wondering why the other side of the normally open switch, C (Yel), doesn't go to the common of the fan motor instead of the common of the condenser? Doesn't the 24V from the thermostat go to the condenser's contractor and then complete the 240V circuit at the condenser?

This question is somewhat confusing. I have made the diagram just a little more clear. Note that the Red and Black horizontal wires along the bottom are 240 VAC marked L1 and L2. Also you are not using the Org on the heat relay for the motor you are using the Brn for the motor with the Prp.

The Red and Blue thinner horizontal wires just above are 24 VAC wires from the transformer. Red from the Yel/Wht lead on the transformer the R on the thermostat using the red wire on the diagram, and C from the Yel transformer is the blue wire that is the common for all the relay coils and also goes to the thermostat. (The blue common to the thermostat is optional and your thermostat may not need a common wire.) So all those Common relay wires can be under one big wire nut or otherwise connected together to the 24 VAC transformer common. Those relays include the compressor contactor, fan relay, heat relay, thermostat (optional), and the transformer. They can all be under one wire nut or several wire nuts that are all interconnected. I also changed the RIBU1C wire color to Yel and Org to match the NO and Com contact wires. I did not change the 24 VAC Coil wire colors because I think you know what they are.

To be more clear about the Fan relay. RIBU1C is the fan relay and the NO contacts will be operating the 240 VAC fan motor by breaking the L2 wire between the power source and the fan motor.

The existing RIB24P is the Heat relay. It is doing the same using the Purple and Brown wires to NO and Com to break the power to the fan motor.

It is important to use the same motor speed on this wiring diagram. If you use two different motor speeds, this diagram WILL burn out the fan motor if both the heat relay and the fan relay are powered at the same time. The Orange and the Yellow on the heat relay are connected to a 24 VAC circuit that operates the boiler side of the system thru the Taco SR501. Not the high voltage side of the system

AGAIN: It is important to use the same motor speed on this wiring diagram. If you use two different motor speeds, this diagram WILL burn out the fan motor if both the heat relay and the fan relay are powered at the same time. The old original equipment wiring system that is no longer connected has a way to use 2 different speeds that will not burn up the motor if both the heat and the fan relays are energized at the same time, but that will be more expensive and time consuming to get you there if you need that. I don't believe you need that so I will not cover that now.  Just use one speed for both heat and cool like I have illustrated.  

Remember to cap off unused motor leads and unused RIB wires separately because they may contain stray voltage that will harm the electrical system if the bare wire contacts a metal part of the air handler or another bare wire.  

Some added thoughts. I am trying to follow what is already there and the way it is wired from looking at the photos provided. It is not the best design but it is what you have and you will need to do the least amount of rewiring.

1. You may need to rewire the heat relay RIB24P so you can use the Org and Yel for the Taco low voltage connection the R and W on the SR501
2. By using the Heat Relay RIB24P as the switch to bring on the boiler system, I have to assume that the Taco SR501 is already wired to bring on the boiler correctly since your heat zone worked fine.
3. I can show you where to add the strap on aquastat wires if you need it in the future. That will prevent the zone 6 fan from blowing cold air as soon as the thermostat calls for heat. That may blow cold air for some uncomfortable amount of time before the heat from the boiler reaches the hot water coil on AHU6.  If the AHU6 is close to the boiler(s) then it may be unnecessary. Just know it is an available option.
4. One low voltage wire may not be needed here

Just put the Red wire it is connected to where the White wire is connected in this picture.

YES To the off topic

OK here is a diagram that will work for you

You need to add a relay for the fan ot operate during cooling or if you select FAN ON at the thermostat. That will be called the fan relay. You can use the existing RIB as the heat relay. You just need to do a little rewiring. So the orange and the yellow from the RIB operate the Taco SR501 on a call for heat.

Either RIB will turn on the fan on the same speed. (If you want to use two different speeds, then that will be a little different wiring so you don't power both speeds at the same time.)

WOW

You have a technician's nightmare on your hands.  You definitely need a control specialist (I was that guy in south jersey when I was working) to understand your system.  

This is what I came up with so far on your problem system

Some of the wires look different in two different photos. I am guessing you have made some changes and photographed the changes so you can go back to the way you found it if your actions do not work. Good Plan!

If I was called to this problem, I would say that you need to start from scratch on that one.

1. Put it back to factory specifications using the wiring harness and thermostat connections that have been abandoned. 
2. Once the Air Conditioning is operating properly continue to step 3
3. Add the needed heat relay in the air handler to operate the zone pump relay (Taco SR501) by way of the thermostat W connection. (that is where you can use a RIB. Once that is in place go to step 4
4. Check for both summer and winter operation with only a thermostat switch over.  

If you are up for that task, I can walk you through the steps

Not a problem Ed, apologies for not providing a lot of info off the start. Didn't want to inundate with too much info as it pertained to the heating, but starting to realize now it likely affects how we connect the AC system.

There are 7 heating zones, each connected to a separate air handler. All of the AC systems are online and now working, except for this current zone (Zone 6). (A few had other issues which I have already addressed - faulty thermostat, faulty zone board, faulty capacitor, etc. Has been a busy past few months troubleshooting these various issues).

Each zone has its own thermostat, except for Zone 4 and Zone 6 which each are zoned systems and have 2 thermostats each (they both have a Honeywell HZ322 with motorized dampers - I just installed 1 last month as its prior zoning board had failed).

All of the zone's heat have been working, though I have noticed that certain zones turn on 1 boiler while other zones turn on the other boiler.

Each zone has its own end switch relay, most are Honeywells, however 1 is the Taco SR501

The 2 boilers only provide hydronic heat to the 7 air handlers.

Hot potable water is on its own gas hot water heater.

Will upload some pictures shortly, thank you again