93 Skylark(I'm going crazy)

Hi, I just recentley started to bring a 93 Skylark Custom 3.3litre back from the dead. The new parts I've added are plugs,wires, icm, used coils, O2 sensor, Vaccum lines, alt, battery cut out cat and new exhaust, and many chassis parts.
I hooked up a tech 1 scanner and found the O2 sensor was no good and replaced it, though it did not throw any codes?? The car still stumbles and missfires once and a while??
The main problem I have now is I was taking it for it's first run and everything was fine until I braked heavy and the engines just cut out. I restarted it fine and as soon as I put it in gear it dies immedialty(can't even give it a nautral drop). As the car runs in P or N you can hear a gear or something grinding in the transmission. If give it about 30 minutes it drives fine again until it warms up. The scanner even shows the tcc is off???(all this takes place at speeds of 60 km/h)
I already hate this car, does anyone have any ideas why the scanner says it is still running lean when everthing else is normal and why she won't drive in gear?
I appreciate you spending the time to read this, any help would be greatly appreciated, Rob.