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1.The header has no swing joints which could possibly damage the boiler. However the length of the header is so short the amount of expansion may not be enough to cause an issue.

2.The header is pitched wrong (as you mentioned) but the amount of condensate in the header is not much so if the boiler is quiet skip that

3.Same with the indirect. If you are getting enough hot water leave it. but the indirect

4.The horizontal run on the Hartford loop is too long. Again, no noise leave it

5.I do not like the safety relief valve on the long horizontal tapping. The relief valve must be mounted upright and should be directly on the boiler

6. I have no Idea what the xtra low water cutoff are for.

The guy that installed this never reads an install manual "I have been doing this for 40 years" Yeah, 40 years of doing it wrong.

If it seems to work ok, I would leave it alone except for the two things I am most concerned about.

The location of the safety valve (which may be the skim tapping)

and the header with no swing joints.

If you read the manual, it mentions the safety valve being vertical

it shows swing joints and a 3" header (depending on the boiler size)

It shows not to do a "BULL HEAD TEE" with the steam outlet between the boiler tapping's.

I think your skim tapping is below the black switching relay on the left side of the boiler. It's an 1 1/4" tapping according to the manual

The only way to escape the rabbit hole is to not start down it in the first place. (Or maybe kill the red queen, I forget. It's been a while.)

Like Br. @Jamie Hall said, if it ain't broke there's no need to start fixing it.

Well… there are a number of things which aren't really right, but —

You mentioned the bottom line. It's working, giving you good heat and apparently not bugging you with noises or other nuisances.

So, in my view, if it ain't broke, don't fix it.

I would look at the pressuretrol; it may be set higher than it needs to be (ideally it would cutout at about 2 psig or a bit less). That's easy.

On the indirect piping: you need as much head on the inlet side of the pump as possible, so having that come from the bottom of the boiler, though it seems odd, is probably not a problem at all (the boiler water will be pretty well mixed to the same temperature throughout when the boiler is running).

On skimming. There may be a helpful fitting somewhere — but see my first comment. If it's working… leave it alone.

As much as I agree with " So, in my view, if it ain't broke, don't fix it. ". . .

And as much as you have the itch to get it set up as close to what the manual states as possible and the boiler is not too old. I would wait to Spring to do the work. For two reasons, time to plan over the winter, planning on what needs to go where AND if something unexpected happens you have all summer to get it straightened out. I don't like messing with stuff that is not urgent prior to or during the heating season.

If the water line is fairly stable when steaming and the system runs quiet it may not need skimming.

How many gallons of water is this ???!!! 311 ? Is there a leak ?

Bingo. Was required for recertification of the boiler room after having sat unused for so long.

Figured I would share my steam library. Just a homeowner here. I would like to try to find a print copy of a 1943 Webster catalog if possible and are there any other recommended books I try to get?