Dowayne,
I think 1/2" insertion would be enough. Can't answer you question about JB weld with fiber rods though.

Just as a side note, when I worked for Hughes Aircraft some years ago, we did an analysis to see how many threads engagement were required to equal the shear strength of a bolt or screw. The answer might surprise you - only three! In other words, if you have less than three threads engagement, you can strip the threads under stress. But with three or more, the bolt will shear first. Of course, this is assuming that the material you are threading into is the same as the bolt or stronger, which wouldn't be the case with JB weld, but 1/2 engagement for a 4-40 thread is 20 threads. That should be plenty as long as you get a good bond to the fiber rod.

Russ.