Electrical/computer problem with 2000 Jeep Grand Cherokee Laredo?

Some of you may recall the many questions I have posted regarding my car in the last 10 months...well here's another!

About 2 months ago I took my car to a garage to have a head gasket replaced, thinking this was the problem after my Dad looked at it. They tell me once the head is off, that I need a new engine. So I bought one with 50,000 miles (my car has 106000) and my brother installed it. Prior to taking it to the shop, the whole engine shook violently and the dash lights flickered.
Now that the engine is in, that problem still exists. My brother has triple checked everything and suggested I take it in again to have it checked out. They tell me it is probably electrical or I need a new computer, but want to charge me to figure it out of course.
I guess my question is, what would cause the computer to be bad if that is it? Is this normal for a jeep that is 8 years old?And what kind of price range would I be looking at to replace it? I can't junk it either, I still owe on it.