I second what has been said about Marlin Crawler
. I put one of their clutches in my 86 4Runner and it was great! I don't have personal experience with URD
's clutches, but I know the rest of the stuff they make is top notch! Regarding the OEM clutch, my buddy has 310,000 miles on his 2001 Taco 2.7L with the original clutch and I have 140,000 miles on my 2002 Taco 3.4L with the original clutch as well.
About the flywheel, I would replace it, Marlin Crawler has them for around $120. Or at the very least have it resurfaced, you do not want clutch chatter.
Also now would be a good time to check out the condition of your slave cylinder and throw out bearing! And i'd inspect the rear main seal for leaks while I was in there.
Just my .02!