So I just replaced the brake master cylinder on a '90 Accord (great DIY on this site, BTW). I did get an aftermarket MC from Autozone (I needed it today). The shaft on the back of the unit is the same length as the one I took out.
All went well but I needed to adjust the freeplay (what a PITA). Anyway, The pedal feels good and solid until I turn on the engine. It then gets mushy and if I push hard enough, the pedal goes almost to the floor and it feels like it's bottoming out on the MC. I adjusted the freeplay both directions, but it doesn't seem to make much of a difference. One thing I f'd up is that I didn't realize that the seal on the back of the old MC was still on the booster when I put the new MC on. Will this make a difference? When I went back and read the DIY MC removal thread, that's when I figured it out (I guess I should have read that instead of only the installation. Oops) There seems to be enough room in the end of the booster to accommodate it and the MC bolted up flush with the booster.
The freeplay thing is confusing. There is the initial play in the linkage, then about 1/2 inch before it gets a little more solid and then another point when it gets harder (all this with the engine off). I get about 1.5 inches pedal travel with the engine off. When I fire her up, then I get 2.5 - 3 inches. It feels spongy. The brakes work fine and the pedal doesn't sink like before I replaced the MC, it just doesn't feel solid like my S2000.
I tried searching for the answer, but couldn't find it. So here I am.

 

Sounds like there's still air in the system.

Did you go back & remove the extra seal? I'd do that first. You might have enough flex in the tubes to do that without opening the hydraulic system.

 

I would definitely go back in and remove the extra seal first (I know you don't want to hear that). Then bleed the brakes.

 

Thanks guys. Tonight I'll get that extra seal out. I always check for that when I change my oil filter, but this looked like part of the booster. And I'll re-bleed the system. I hope I can get the adjustment rod back to where it was before I started adjusting it. I went both directions with it, so I don't really know where I started (dork).
The pedal freeplay is checked with the engine OFF, correct?

 

I don't know about that one. I never had to adjust the pedal freeplay before

 

And don't if you don't have to. After reading posts about how on some aftermarket MC's you may have to adjust it, that was my next logical step. I felt that we did a good bleed job but there was too much freeplay. Well, guess what. If the adjusting rod is too tight, it WILL lock the brakes on. I took the side streets on the way home at lunch, and sure enough, the car starts slowing down. I pop it in neutral and it comes to a stop. I'm glad I brought some tools with me in case this happened. Now I'm wearing my good work clothes and I'm there on the side of the road crawling under the dash, sweat pouring down, adjusting that dang freeplay for 45 minutes until I could finally get the car to roll in neutral. What a pisser.
Tonight it's me + beer vs. the Accord. We'll see who comes out on top. I hope that once I get the brakes bled REAL good, that I'll be able to adjust the freeplay correctly using the steps in the DIY section. I wish I never would have touched it because I don't have a referance point on where it was to begin with. Live and learn baby, live and learn.

 

Thanks for all of your help guys. Re-bled the brakes, got the extra gasket out and adjusted that damn brake pedal linkage. All is perfect now and Mom is happy.

 

Thanks for the update. When Mom's happy, EVERYBODY's happy.