I used to run into this problem a lot on my D-44 that was in my fullsize chevy. I always opted to NOT weld them in, -just because.
It is possible to bend the yokes, -they are very malleable and can bend, -but usually if you bend them too far, the caps won't even go on to the trunnion of the u-joint cross, -so I seriously doubt that's the case with yours.
I used to re-use my old spring clips, because it always seemed that the new ones fit way too tight. One other thing I used to do was grind the clips down to make them a little thinner.
One time I managed to get a new set of spring clips in (just barely), but it made the joint bind really bad, -so in went the trusty "used" clips, and all was well.
Another alternative to welding is to use green loctite (the slow-set stuff). I used that for a while and never lost a cap, -and they aren't too terribly difficult to remove with the help of a propane torch.
My .02