After doing extensive research about powertrain control modules I have concluded that the safest procedure is to simply purchase a replacement which I have found at DeadJeeps.com. For my '94 YJ, it will cost approx. $350. and DeadJeeps informed me that it will arrive already programmed, thus a plug-and-go install. My mechanic warned me about shipping my defective unit for a rebuild for a couple of reasons: 1) if it gets lost in shipping, you are SOL and you have immobilized your rig until you find an adequate replacement; 2) In the opinion of my mechanic, there are a lot of questionable rebuild shops out there who might simply switch your unit for another. Dealing with an eBay shop gives you some sense of security as eBay will back up purchasers with their own guarantees.
My old module still works fine other than it occasionally sends a surge to the alternator which then triggers the check engine light on the dashboard. If I turn off the engine, the light goes off and often stays off for days (until that infrequent surge happens again). My mechanic says there is no harm in merely continuing with this procedure, however, I am willing to spend the $350 and bring the electrical operating system up to standard.