Were not trying to chastise you, just trying to help. The one thing though, get a factory service manual. Be sure to measure the clearance between the rod sticking out of the booster and the piston in the master cylinder, I don't think the service manual gives that measurement. Let us know how it turns out.

I agree. Believe it or not and despite the implied stupidity of my questions/posts though I do have somewhat of a clue. The service manual says remove front and rear brake tubes from master cylinder (residual pressure valves will keep cylinder from draining) remove nuts attaching master cylinder to brake unit. Remove master cylinder from unit. No other details given. Despite these instructions I will likely still remove all the fluid from the chambers first and cap the lines. I was looking for more detail on what if anything I need to do to the back end of the master cylinder. New ones come with a plate over them.

You're doing fine bro. I would suggest (1) taking the nuts off of the (4) bolts that secure the MC to the booster so it ready to come forward/off. (2) wrap a BIG shop towell around the lines/under the MC to catch fluid cuz some WILL drip (3) unbolt the nuts/pull the nuts/lines out of the MC (4) Immediately pull the MC foreward off of the bolts & and as soon as it is free of the bolts tilt it (the ports) up to minimize the mess & tilt it forward some as it is leaking out the back side also. Dont tilt it a whole lot as I am assuming the bowls still have some fluid in em & covers ain't always tightly sealed. that'll get the mess out of there & be a start

You can buy fittings at auto parts stores that you can install in the master cylinder outlets when you remove the lines, and in your new master cylinder after you bench bleed it before installing. This will keep fluid from dripping out of the outlets onto your car when you are removing and installing master cylinder.
NAPA and I'm sure some other stores sell a neat kit that contains fittings, tubes, plugs and clips for bench bleeding master cylinders that will make your job a lot easier.
One of the outlets is 1/2-20 and the other I'm not certain off the top of my head if it is 9/16-20 or 9/16-18.
Search Youtube for very helpful videos of many automotive repairs including working on master cylinders.
A couple helpful hints I would give are if you don't already have them, get some flare nut wrenches. The metal the fittings are made of is fairly soft, and it is all too easy to round off the flats using a standard open end wrench to loosen and tighten them. And bench bleed the master cylinder before installing, rather than trying to bleed it on the car. If you do a good job of bench bleeding, you are usually good to go after installing the master cylinder on the car without having to bleed at the calipers and wheel cylinders.

In the process of bleeding the new master cylinder. Front reservoir pretty much bled right away. I've been pumping and while and haven't gotten any fluid flow from the larger rear reservoir. Is this normal?

I told you to find a shop.

The shuttle in the combination valve is stuck.

Open up your factory service manual and read how to bleed the brakes, you do have one right?

I'm not taking it to a shop. I have a service manual and know how to bleed brakes. Maybe you didn't really read my post before you replied, but bench bleeding a master cylinder doesn't involve a combination valve.

Are you bench bleeding on the car or in a vise? Shouldn't make a difference (but trying to get a handle on this) if you are depressing the pushrod enough & you are cuz the front port is flowing (& "front" is the front smaller reservoir not the "front discs". Holler back.

As RapidRobert has pointed out bench bleeding both sections of the reservoir requires you to not only give short,shallow pumps but also pushing the piston completely in to the limit of it's travel and working it a little while back there...This will bleed the other half of the MC...

While Supercuda got a little ahead of you he does bring up a valid point on what's to come when you bleed the lines and rest of the system..Rather than write a book here's a helpful page to learn about the procedure..

Not on the car, on the "bench".

& I reread your post & you did say the large rear reservoir for the front discs ain't bleeding & that is strange cuz that piston is gonna be pushed before the one ahead of it is. No way the disc half of an OE MC would have an RPV in it but with this being a strange case (assy line errors happen) & I would stick a drill bit into the brass inverted flare cone in the port & you'll feel it if it is in there as it is just a piece of neoprene and a spring. Take ya 1 minute EDIT yeah "bench" bleeding has morphed into if it is being bled in the car or in a vise or on the bench as long as the hard lines in the vehicle ain't hooked up to it then that is considered bench bleeding as there was probs with people bleeding the corners WO "bench" bleeding the MC seperately first then not being able to get the air out (would pump up & hold briefly for a few seconds was the symptom). Holler with any news. MORE EDIT With more thought I dont there could be a RPV in there but this is a strange one

Are you sure the correct parts were used in the rebuild? If the Mk551 kit was used it has the incorrect primary piston and will not work.

I do have correct kits and pistons.

I haven't rebuilt the original yet. I got a new Raybestos MC36283 unit and swapped it out. I'll shelve/dig into the $$$$$ original at some point. Only thing to use from the MK551 to rebuild the original as far as I've read are the seals.

I used a vacuum pump to suck fluid through the unit and to bleed the 4 corners. All seems good.....we'll see.....

Here are some pics of the new unit installed.

Secondary piston is the same as the e-body also

Car back together all seemed to be good on the test drive. I also had a chance to dig into the original master cylinder. Here are some pics. I think it actually looks pretty good inside but not sure. Thoughts?

Cant tell (bore condition) from the pics. I just splurged and spent some of my accident money & one item I just got was a HF borescope & that is the neatest tool & have ever used! I feel like a surgeon. I'd clean up the bore then visual for pits & flexhone lightly (they have a specific procedure (drill speed etc) then clean it out & lube up/install a new kit. if no severe pitting the odds are you will turn out fine

No pitting. I'll check into the bore scope. The worst place is the very end where it looks like the piston sat stagnant for a while and it kind of left a mark into the bore a on the bottom. Actually looks worse in the pic than it is. Likely where the leak was coming from though. It's the second picture. Apparently I can hone up to 0.02" off and be ok. That's not a lot. The rest of the bore is great. I doubt I'll put it back on the car and just rebuild, repaint and maybe put it in a display case and put it on my desk to look at and show off to friends since they are so valuable🤑.

I agree with him not wanting to let some repair shop touch his classic car on the chance that they might screw it up in some way. My whole family can tell nightmare stories that are not even believable! Moparts has been and still is a terrific learning tool for me personally, and I am extremely thankful to those members who have helped me! It's vey easy to find someone who is smarter than me... uh, um, please disregard that last part.

What size flex hone should I get 1"?

Already done! find/measure the bore dia then call brush research manufacturing 323 261 2193 & ask them which one (size/grit). EDIT You might get on there website (it'd be free) & see what you see. if the bore is a certain dia you need a flexhone that is slightly bigger (they'll have an ans for you). they want you to use their oil (not sure how critical that is) they want a certain drill speed and a certain number of strokes per minute. BRM has a list of OE and aftermarket users a mile long.