Two Questions on a New Radiant/Infloor Install

I had an in floor system installed when I built my home 12 years ago. I went cheap and it cost me. Several issues but we eventually made it work. It was an open system and was run off a 130K Polaris. It always bothered me so this fall I decided to clean it up. I got several estimates and made the decision to do the majority of work myself. I drew up the schematic with the Boiler tech advisor and went to school on hydronics. I have a whole new respect for the really good professionals out there. I piped the new system Primary/Secondary at 1". I have 3 new zones...one 8' baseboard run and two wall hung vertical radiators. Those are run off the top manifold. I want to run those at 170-180deg. After the mixing valve I have the old/original manifold run to the in floor system. Water temp set from the mixing valve to 120deg.

I ran the new radiant zones to a Taco 3 zone relay. I have one bedroom in floor run to a single zone relay and the other two in floor runs connected to 2 Goldline SP-30 Set Point Controls. I have connected both zone relays to the TT connection on the boiler. I hired a local heating/plumbing company to come out and run the 3/4" gas line to the new boiler and perform a combustion analysis. I also requested they fill the system zone by zone and purge all of the air. He was on-site for 8 hours yesterday and called me when he left. He was a very cordial professional and was not condescending about my work...even though he had some concerns and questions. Not the way their company designs pipe run/systems etc. He said the system was up and running and putting out heat. My wife said radiator in master bath was warming up.

I got home and hour later and went down to check his work and see the boiler in action. I noticed something wrong immediately. Pumps were overheating and sounded like they were running dry. 2 radiant zones and the basement in floor. Pumps too hot to the touch and supply piping cold on push side of the pump/warm on suction side. Pressure on Secondary piping top manifold read 5psi. Eventually went to 0psi. First thought was major air still in the system. I shut everything down and went zone by zone to see what kind of air was in there. Quickly found out there was a lot of air remaining. I spent a couple of hours letting the zones flood until I could see no air pockets bubbling in my 5 gallon bucket. I let it run several minutes each after the last sign of air. I was able to get 5 out of the 6 zones air free. I could not get one of the radiator zones unblocked. There was NO water coming out of the drain end on the manifold. I ended the night with that one zone unfinished...frustrated.

Two questions...

1) How can I get the air out if it remains blocked?? Any tricks of the trade?

2) Can I connect the Goldline SP-30 set point controllers to the TT connection on the new boiler? There are 6 low voltage connections on the controller (C, R, 1, 2, 3, 4) as seen in the attached pic. I am wondering if 1/2 are contact points that would close the circuit and message the boiler the in floor sensor is calling for heat and the pump is running? Please note the awful wiring job was done by the original installer. I have corrected with conduit and box connections on the new install.

Thanks in advance for the help. I welcome constructive criticism on any of the project. My biggest regret is that I did not size the secondary line at 1 1/4".