Back, but not really kickin'...

Well, I'm sure that some of you were glad to see me go ;-) but here I am again. Finally got back online, but my car's a different story. I have now replaced the whole fuel system, checked all the sensors (all good) ran a diagnostic (no problems), cleaned out the air intake system, checked the timing (no problems), replaced all the vacuum hoses and the sort, and checked all the wiring (again, no problems). Unfortunately, I still have a bad shudder in my engine. I was wondering if anyone had ran across that before. Also, I added quite a bit of stereo equipment, but that's not the problem, and the alternator and battery are great. Two more things: Can anyone give me good directions on flushing my tranny, as well as flushing my coolant? Thx guys...
-Shifty