It's only as difficult as the actual work. Realize, of course, that depending on the mod, switching out one big thing can rain down a bunch of smaller things. Example: I switched KELLI GIRL over from fixed-pitch to a constant speed prop. Changing my engine setup from FP to CS prop required installing a new governor, new blue throttle cable/knob, oil line, prop shaft plug, etc. Remember, if you impact the weight or CG, you'll need to do a new weight 'n balance for your POH (and that's easy, too).
Also, depending on the upgrade you may have to return the aircraft to Phase 1 test. That depends on whether it's a major mod, etc. Your aircraft's FAA Experimental Operating Limitations will spell that out, and then it's a simple paperwork drill. Example: Changing my engine setup from FP to CS prop required 5 hours of Phase 1 with a straight-forward letter to the FAA. Beyond that, it's a matter of actually doing (or getting someone else to do) the work.
Thereafter, it's pretty much all yours.