Lincoln/Mercury Repair: 95 Merc Villager electrical, cottman transmission center, style cars

Question
Just rebuilt the engine on my 95 villager.  Runs great, but with two issues one major.
Major issue is that the battery won't charge or hold a charge.  Thought it was the alternator.  Replaced that yesterday then it died again.  About 20 - 30 mins drive time then warning lights come on, tach, odom, speed, all stop working and the engine wants to stop and usually does until I charge the battery.  Battery is brand new too.  I am thinking a bad ground some where but can't find it.  I checked all the fuses under the dash and they are all good.  After the amount of labour I have put in I am getting frustrated that it runs but I can't keep it running.  Then minor problem is when it is running the tranny shifts hard now.  This didn't happen before.  Friend that helped me with the rebuild tells me the computer takes time to adjust to the new engine and will sort itself out??
Thoughts.

Answer
Hi Scott,

I suggest having the vehicle scanned for DTCs. A local Cottman Transmission center will do it for free. It's not OBDII so you'll need a somewhat experienced guy to get the codes for you. It sounds like a faulty alternator to me. If you feel it is a ground try using a ground strap from the engine to the frame. Grounds can go anywhere so that is an easy fix if it is the problem. Also, the hard shifting could be related because it's not giving enough juice to the transmission. Low voltage plays hell in these newer style cars. Try to have your van scanned so we can see what's going on and we can move on from there.