This is totally a shot in the dark but it may be your problem.
Sometimes the flexible gauge cluster circuit board can develop cracks on the wire pathways (not sure what to call it) and make your transmission not shift or shift erratically. I was having transmission issues (wouldn't shift out of 1st until it warmed up) and this was one of things that was suggested. It didn't fix my issue (mine is something mechanical in the tranny) but it *may be your problem.
The reason why it may be your problem is the people with the shifting problems also reported it acting up when they would turn on their brights and other stuff. And the "R" would be faintly lit up on the cluster even though they weren't in reverse. Not everyone had the symptoms and sometimes the symptoms were intermittent.
Let me see if I can find it in my post and I'll link it on here.
http://www.toyota-4runner.org/3rd-g...ng-when-cold-yes-i-know-its-normal-but-2.html
Post# 29, like I said its a long shot but worth checking out at least.