Motor work is only big money if you are afraid or unable to do the assembly work yourself. You can get cases and cylinders ported for about what you will drop on a used factory pipe, and less than you would drop on a new one or a new aluminum charging flywheel. Tim Z and Chris Newmiller both do excellent work and have very reasonable prices. Art Gomez of BlackJack (formerly jetworks) also does amazing work, but a little more pricey.
For more bottom end--Throw a factory limited pipe on there (it was my experience that the R&D increased bottom end very little if at all), have your reduction nozzle bored to 82mm, find a CDI out of a 96+ SXi or '03 SXR (skip the fixed timing advance), mill your stock head, find some dual SXR carbs or a single 44 or 46.