That's an odd one. Did you climb under there and measure the amount of release while someone presses the clutch and goes thru all gears? Is 2nd and 3rd within standards but not 1st and reverse?
How much pedal freeplay is there before clutch starts to engage? I usually go with about 1" for my 11" disc. If you got worn linkage or worn anything else, you may need a little less freeplay.
Did you install a new pilot bearing on that 261?
Is the bearing retainer worn on the 3spd? These could cause you're problem.
It just doesn't make sense. If the input shaft and bearing retainer is the exact same as 4spd, it should work.
You gotta start looking at what's different in this setup: The 3spd and it's related parts i.e. input shaft and bearing retainer, clutch linkage, clutch fork? and adjustments.
This is a silly question and you probably wouldn't be able to get it in any gear but, did you install the release bearing backwards? I did that once when I was in a hurry.
-David
Kustoms-and-Sleds