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If there was no residual pressure in the system then it’s probably not a plugged spooge hole in the master cyl., if it was me I would use a .010-.015in piece of shim and run it between the brake shoes and the disc on both sides of each disc to make sure you have clearance w/o the brakes applied,

There should be clearance but I suspect you don’t have any on one of the disc’s , there is NO wearing the pads in ! On the brake fluid/lube, just use clean DOT 3/4 brake fluid , nothing else. You cannot mix dot 3 or 4 with any kind of DOT 5 brake fluid, they are not compatible and will cause things to lock up. I have nearly 30yrs working in brake engineering and all that we generally ever used for assembly or lube was clean, fresh brake fluid. Period !

Pulled the master cylinder apart this evening, spotless inside.
I did notice the brake lever, which came with it, was preloading the piston by about 1.3mm, other than cleaning and reassembling I ground the contact point on the lever down till there was no preloading and that seems to have taken care of the dragging brakes.

I bled them and am not really happy with the lever now(it was better before but that was I suppose an artificial better since the pistons were not retracting), I can juuuust almost put the lever on the handgrip with moderate effort though it does start having resistance well before that. This is with new stainless lines so it's not old rubber swelling or such.
Too late for a test ride, maybe tomorrow.
I read a suggestion to pull the calipers and bleed them with the bleed nipple at 12 o'clock since small bits of air can be trapped in there, might give that a shot.

I still have another master cylinder ordered, be interesting to see if it preloads the piston any.
Might try it, we'll see.

I feel like I should buy a GL1100 master cylinder used and rebuild it, I've read they fit and work alright on the late GL1000.
Any thoughts/experience?

There are a lot of places where a tiny bubble can lodge. You can often induce a bubble to rise into the master cylinder reservoir by tying the brake lever as close to the handlegrip as you can, turning the bars until the master cylinder is in the highest possible position and leaving it like that overnight.
I do this whether I think it needs it or not and it usually makes at least some difference.
I use a velcro strap for tying the lever; Some people use zip ties.

I have had some success gravity-bleeding front brakes by doing whatever it takes to orient the system so that the lever end of the MC is at the highest point, with no loops or high spots in the lines between. This has sometimes come to leaning the bike against the wall, and-or rotating the bars way out of normal position. The buckhorn bars on a 1200 are particularly hard to do, since the MC points up instead of down. Doing this allows the air to naturally rise to the MC where it escapes through the relief hole. You do have to agitate the fluid by squeezing the brakes repeatedly, so that the bubbles have a bit of a push to rise. It takes a while.

I saw a post from someone that suggested rotating the brake calipers such that the bleeder was at true 12 o'clock and bleeding them in that position with the piston supported, thought I might give that a try. Really does feel like air in there despite a thorough normal bleeding. I tapped on the calipers a bit here and there with a rubber mallet that sometimes will dislodge air bubbles but no luck. I need to make a pressure bleeder attachment for this thing, manual brake bleeding kinda sucks after using a pressure setup for the last fifteen years on cars lol..

Try tying the lever. It has helped many over the couple of decades since I first heard about it and it is the easiest thing to do. And even if it doesn't help it can't hurt.

Will do, thanks guys

I ziptied the lever back at lunch and checked it this evening and sure enough, it feels quite a bit better.
I'll leave it tied back this evening just for the heck of it, it's about as good as it was now.

The question now is do I leave it be or source a 1100 one and rebuild it.
Kinda leaning toward the latter.

If this one works and is fairly new why would you consider buying a 40 year old one and rebuild it in the hope that it will work as well as what you have?

BTW, if you do decide to change to a GL1100 master cylinder 1) make sure you replace the sight glass as part of the rebuild and 2) do NOT get one from an '83 because the linked brake system uses the rear master cylinder to operate the rear caliper plus one of the front calipers while the front master operates only the other front caliper.
You need a master cylinder that will pump a sufficient volume of brake fluid to operate both front calipers before the lever reaches the handlegrip.

The mounting angle of the reservoir isn't great on the aftermarket one and I can't buy a rebuild kit for it, or even a rubber gaiter for the cap is the primary disadvantage of it. That and I still don't have any reason for why it was dragging the brakes, it was like new inside and I didn't change anything, it just magically worked when I put it back on which isn't overly confidence inspiring. If something can magically fix itself it can magically un-fix itself too.

Looks like the factory stuff still has parts availability including the reservoir and sight glass. If this one acts okay for a bit I'll likely leave it and put a replacement on the shelf for the next time I feel like spilling brake fluid all over.

The reservoir angle I'll go with, but without looking at the 1000 and 1100 handlebars together there's no guarantee the 1100 one will be any better.

As for the dragging, didn't you say that adjusting the lever so that it didn't press on the piston at rest was what fixed the dragging? If so, I doubt that the part you ground off will grow back so the problem isn't likely to return.

That's the theory, yes. I wasn't awake yet earlier.

I left the lever tied back last night, popped it loose this morning and the master cylinder piston didn't spring back.
Fiddled with the lever a bit and it finally released, seems okay now and the pull feels even better.
Kinda odd..

As a lifelong mechanic I have an inherent distrust of aftermarket parts, especially ones made in the far east.
These are a pretty simple part and I didn't see anything overly objectionable when I had it apart other than they sized
the lever press point on the piston wrong. I'd just plain feel better with an original Honda part on there, if I can find one the bore isn't overly worn or eaten up from age. We'll see.

Note that the original Honda part came from the far east too, and I believe that Honda sources a lot of their parts from China & other places other than Japan these days.

FWIW, I've had a China/eBay master cylinder on my 1100 for 9 years and the only complaint is that the sight glasses in them start to get soft after a few years. I don't consider that a big issue because replacement sight glasses are cheap & easy to install so I just do that when I'm replacing the fluid (every 5 years).
I had a similar master cylinder on the CX for many years too and only replaced it when I replaced the entire front brake, starting with a caliper that I hope will withstand road salt better (long story here) that needed a master cylinder with a different bore. The new master came from China via Amazon for $20CAD (less than a rebuild kit for a used one) and it seems to be OK so far.

Yeah there isn't a lot going on in one of these, couple holes, couple seals, the piston was brass or something that looked like it. I'm sure anything made now is a "world bike" just like cars are, I'd assume in the early 80's they were still producing them locally as obsessed with quality as they were but who knows.

Just for later reference, the replacement aftermarket one I ordered preloads the piston just like the one I had on the bike did.