My 88 4runner driver door has been driving me nuts for a long time. I have to pull the handle two or three times from the inside to get the door to open. The outside handle works fine. I found a post somewhere recently where someone had the same issue and it was the metal connecting rod between the handle and the latch. I couldn't find it again to save my life, but the post mentioned that Toyota had some foam in there to keep the metal rod from lifting out of place or something. That person drilled a hole in the door and added a zip tie (I think) and that's probably better long term.

What I did, if you don't want to drill, is to wrap some foam (I used the existing foam) in some Tesa tape. If you wrap it on thick enough it slides with the metal rod but doesn't "lift up". VIDEO HERE

It's simple and has been covered before, but it worked for me. Also, if you have the nicer door panels on the 88, there is a hidden screw behind the door handle trim that I didn't see called out in the manual or anywhere else.