In the grand scheme of things, I doubt that an extra few thousandths of end play on the axle shafts would ever cause a problem. However, if the idea of running a little out of spec causes you to lose sleep, why not have a good machinist make a spacer block from oil hardening tool steel thick enough to get the clearance within specification, get it cherry red with a rosebud torch, and quench it in a bucket of motor oil. If it was my truck, I'd already have it reassembled and put a bunch of miles on it!
Jerry