Keith, by "temp drift" you simply mean that the tank wasn't truly staying at 100F for the whole 3:15 minutes, right? Are you suggesting to stick the thermometer in between agitations to keep an eye on it?
Well, no, you probably don't want to have to look at a thermometer during the 3', but I would first investigate, with lights on, what happens when you bring ordinary water up to temp and then pour it in and out etc. You just have to satisfy yourself that your procedure keeps the right solution temps throughout. By the way, I use stainless vessels and noted that when pouring my solution into a cold vessel, the temp dropped appreciably. So I preheated my vessel, problem solved. I also saw appreciable temp drift when tray dev'ing c41 LF film, even with a temp-controlled 'bain'... something I am still working on. For e6 its more critical, I need to install a temp controller with a thermometer directly in the developer.
I like Ron's suggestion to scan your negs as positives... experts can diagnose many ills that way.