I haven't worked on an 86 before...but what module are you talking about having to remove? The basic's of an MSD box is that it goes inline between the coil and the distributor, then you run a hot and a ground wire for the MSD box....which buying the wiring harness that they make for your model car really makes wiring it in a breeze. I don't know if it will happen with your car, but sometimes the signal that comes out of the MSD box isn't one your computer will understand for some reason...my 92 was this way and the tach would bounce around like crazy and the Service ASR (traction control) lights came on. MSD makes a simple adapter that you install and it should clear it up and have it running like it should. I've seen this in a couple other cars that I've helped install them in, I really don't know what causes it or what's wrong/different about the signal coming from the MSD box, but this is the only side effect that I can think of at the moment and it's a very simple fix.
Actually there is one other side effect that I know can happen, and that's radio buzz. Make sure you have good connections everywhere, solid grounding where it's needed and a good set of plug wires and you should be fine. I think most of the time when I've ran across this is when someone had tried to do a rush job install instead of taking time to wire everything very solidly the first time...which to me was always kind of ironic or something because it's not a very long job anyways. Also if you're considering doing a tune up on the car before or during the install, you'll want to run normal copper top plug's with an MSD box, not any of the platinum/irradium/expensivium gimmick plugs that are out there as an MSD box will create too much spark for them to handle and burn them up.
