While I don't have any experience with 5-speed 4runners, the first thing I would do if it was mine is drain the trans, and refill it with Redline MT-90 Manual Transmission fluid. Then I'd know for a fact that a great full synthetic fluid was in there.
Besides that, I'm not much more help. All my previous vehicles that have been manuals have always been harder to put into gear when they are really cold, but not imposssible. And I always used a good full synthetic fluid in them too.