Check for vacuum hoses that may have been disconnected when the master cylinder was replaced. It sounds like you may have an IAC that is on its way out... check the resistance of the coils as specified in the FSM and/or disconnect it and see if the stalling goes away. If it runs good at anything other than idle I doubt your injectors are a problem. Take a look also at the distributor rotor and inside of the cap. A long shot, but I had a problem with mine where the rotor was cracked and providing a low-resistance path to ground. It would idle, but cough and try to stall when I gave it gas, but would eventually catch and then run fine... until the next red light <img src="/forums/images/graemlins/rolleyes.gif" alt="" />

Good luck!

Eric W.