This is from a member on yotatech:
3rd Generation factory front woofers are 6.75" when measured all the way across the mounts, and the brackets must be slightly modified to fit a 6.5 correctly (without stress on the mounting ring and the screws in straight). I know this is true from actual measurements from a '96, a '98, a 2000 and a 2002. I have seen them listed from several reliable sources as 7" and I have stated that several times in other post. Tonight I actually measured the removed speakers I have in my garage and it was dead on 6.75".
As far as the rear goes it is a little confusing. The factory rears should probably be considered 4" as that is the speaker size, but the large mounting ring and cardboard baffel make the speaker "assembly" more like a 5.25 inch. I have a 4" set of Alpines in my Jeep and the speaker cone is the same size as the 4runner cone but the mounts vary by about an inch. You cannot just swap them for a 5.25" using a factory bracket for sure in the '98 and 2000 that I have worked on, but they can be modified to take a 5.25" or a 6.5". If anyone wants more info on this I have pictures and some recommendations, but I know we are trying to keep this neat.
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I have 6.5" and 5.25" Kicker KS series (component front and rear) going in in the next month or so when I get around to it.