Update...not only did the check engine light come on today, but it just died again. It looks like everything that I did so far did not help.

Can you get that code?

Will have tomorrow, going down to see engine installer

Just came from the shop, this code was 0336 (I think) "loss of crank signal or out of range". This was the first time that this code showed up. He did a crank relearn as suggested above, he also admitted that they never did a relearn when they replaced the motor. His theory was that the crank sensor doesn't need relearned unless the balancer was removed, which in this case was not removed. He was very willing to do whatever it takes to get this thing running. His suggestion was to run the car and see if it's OK. The next step would be to replace the crank sensor or check the wiring from crank sensor to the computer.

You're on the right track. If the CASE learn doesn't fix the problem (and it may), the crank sensor is your biggest suspect.

Be advised that the crank and cam sensors are on the same circuit, feeding through each other and through the ICM (under the coils) before going back to the PCM for the fuel and spark timing.

You will find most mechanics find that if they start the car and it runs..that the CASE learn is considered not needed. It does a true learn and helps the PCM know TDC

It's been 3 days and not a single problem yet. Of course it's a holiday weekend, I'll know for sure next week when the wife starts putting some more serious miles on it. I have my fingers crossed as I type this!

He's got that wrong... You have the same computer and a replacement engine.... The chances of the the new engine having the crank at the same spot that was learned from the factory is almost next to impossible... The car can and in most cases will run, but not properly as the cars computer does not know the true location of the crankshaft position...

Let us know if the CASE learn has resoved the issue ;)

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Well...it's been almost a week and guess what.....CHECK ENGINE LIGHT!! I took it to the shop and it read the same code as the last time, loss of crank sensor signal or out of range. Looks like I need a crank sensor. Anyone know the correct number for a '98 Bonneville SE 3800 crank sensor, and is this something that I can do myself without too much difficulty? I know that there is a cover that gets removed and the balancer gets pulled.