I guess I was lucky enough to get an uncommon d44 axle housing in my Jimmy. I need to install axle shafts and was wondering if I could just cut 1/2" off of a newer shaft? What problems would it cause if I cut it too short?

If you cut that much how much spline would be left? That doesn't sound like alot, but it depends on how much you have left.
What are you talking about "an uncommon axle housing"?
Its either a dodge, pass or drive wagoneer, bronco, chevy, or ford![]()
ALL D44 axles are the same length, sounds like you might be trying to install 10 bolt axles into a D44.

No, they ARE NOT all the same....
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To answer your question directly though yes you can trim splines but its no the best method and as said you're going to face other issues with snap ring grooves etc with stubs. However the end snap ring on a stud is really not necessary as the hubs have their own retaining ring. Lots of us run dana 44s and 10bolts with no outer snap ring.
This is the first time Ive ever heard of this problem and would be interested in seeing how it turns out for you. Im not super well versed in the dana 44 varieties other than the chevy axle but Ive always been under the impression there werent for example chevy axles with a 26in long short shaft and then a chevy axle with a 28in long short shaft from a different year. Perhaps your mismatched in the spindle or hub for the chevy outer?