Charging Problems ***PLEASE HELP****

It all started when the thermostat locked shut and she overheated...
I pulled the thermostat out to get it going and the starter wouldn't turn over.. had lights, ignition, no starter...
pulled starter off.. it's good... starter relay good...
wired a push button to the starter... vrooomm!!!
now it won't charge.... new battery, new (rebuilt) alternator and not enough juice to make a five mile trip to work.

is the starter and alternator connnected in some way? is it in the harness? the computer? neutral safety swith? aaaaaaahhhhhhhh!!!!!!!!

i just want it to start and charge!!!!!

any suggestions on what to check before I take this alernator back off???

thanks in advance..
1994 XJ 4.0 OBDI

check all of the fuses in the fuse box under the hood...chances are that one is blow and not allowing the alternator to power up. May want to check the start relay in the fuse box,too.