On the road again, a few questions
 

After draining what looked like melted chocolate root beer float with cookie crumbs from the brake system, and hot wiring the radiator fan to a switch, I was finally able to take the the car out. I'm really looking forward to many hours of enjoyable troubleshooting of the hundred things that are currently in need of attention.

Question: After a lot of bleeding the brake still need to be pumped. Single push, it travels about 3/4 of the way. Pump it, then it gets firm at about 40% in. Holding it there it doesn't deflate, but let go of the brake and wait a short bit, it needs to be pumped again. Suggestions?

Question 2: what is the best way to temporarily glue the body rubber in place? Doors, bonnet, trunk door, etc. Eventually I'm having the car painted so I'll need to remove them. I'm thinking transparent silicone caulk.

This syndrome looks like the master cylinder seals are shot, or there is corrosion in the cylinder.. How long was the car off the road ? Assuming there are no leaks at the wheel cylinders on the calipers, this is the most likely place. Recommissioning cars that have stood for some time always comes up with things like this. I have been lucky with my MG Midget that stood for 14 years, as I have only had to replace the clutch slave cylinder, the brakes have always been OK. Sure enough, the slave cylinder was corroded where the seal had been sitting and my waking it up 14 years later saw it finally give up the ghost. If you haven't inspected all the wheel cylinders on the calipers then do so now and look for leaks. The rears tend to suffer more than the fronts from heat as they are right next to the inboard brake discs and cooling is not good in that area. I had a wheel cylinder there that eventually seized up and then got cooked and leaked the brake fluid out. You should have seen the trail of white smoke I was leaving behind !! Exchange calipers cured the problem.

It sat forever and a day. I have every reason to believe that the rubber there is shot and I fully intend to rebuild the master cylinder if nothing else out of principle, but it still feels weird. Usually faulty rubber seals on the master feel like the brake looses pressure. Here after I pump it has a good feel and it retains that feel for as long as I hold the pedal down. Let go for five seconds and the next pump goes within 20% of travel to the floor. I'm just wondering if that's something common to this particular weird setup.

Heck even at full pump it doesn't feel like I can lock the brakes. I have the feeling that it is not breaking at its full potential but I don't have anything to compare it to.

Before you spend money, I would check the bleeding process. Your symptoms sure sound like air. Each bleed nipple should have a check valve (ball and spring) to make bleeding a 1 person job. You might check that everything is clean around where the balls seat. Also, I have found that releasing the brake pedal too quickly while bleeding can cause air to leak around the piston cup constantly reintroducing air. Finally, I have large hands and cannot bleed the rear pistons without some disassembly. That means removing the front spring/shock on each side which gives good access to the calipers and makes getting a good seal with the bleed tube easy.

Hope this helps but do not cut corners when addressing faulty components. Your second question: contact cement is not too difficult to remove and I think silicone will fail after some time.

The brake hoses could be breaking down inside and preventing the proper flow of fluid to the master cylinder Or they could be ballooning from the pressure. I would check every component of the system before test driving it on the road. E types are valuable, but your life and those of others are worth much more!