904 shifting strange
How long has your trans. been acting like this? If is since you've owned it somebody may have installed a shift kit in it and maybe it was a poorly designed one. Most on the market today are poorly designed I've found. You can install one in one trans. and it works right then install the same kit in another and have either shift overlap problems or shift timing problems like you describe. The only kit I will ever use again is the Trans-Go kits. They are the most expensive ($50-60) and more work to install but they allways work right because Trans-go did their research on Torqueflites and found you just can't drill 2 oversize holes in a seperator plate and block the accumulator and expect them all to work consistantly.
The way I adjust the throttle pressure linkage is to hold the throttle wide open and adjust the transmission linkage as far back as it will go. That will raise the shift points to their highest and allow passing gear to work. Sometimes it takes 2 to do this correctly. One to hold the pedal down and the other under the hood doing the adjustment.