I have a 2004 Toyota 4Runner 4.7L 4WD. I have been dealing with the same issues that the OP mentioned (rough idling and acceleration, multiple cylinder misfires, won't start etc.) I have had several mechanics look at it and suggest different causes or sources for these problems. But as I work on this I keep returning to this post. I'm going to take it to the mechanic and have him replace timing belt and do a complete check. Lets hope for the best.
Dude. Glad you got it fixed. I picked up a 4th gen V8 with 181,000 miles on it this past summer and no timing belt or anything had been done to it before. Had the timing belt,water pump, etc. Done immediately. Glad you avoided any major repairs to it!