Your D17 will bolt-on a D15 transmission, but there will be some shifter linkage fabrication (you have cable whereas 5th and 6th gen had rods). I don't know if the older engines will swap in, and there is a security immobilizer to consider in the 01-05 Civic.
Other thoughts... you could get the whole D17 Civic HX engine and bolt it in, needing the wiring harness, ECU, and HX transmission. That would give you a learn burn "HX/LX" or "HLX." Increase the complexity of that idea further and get a 1992-1995 CX/VX trans.
More simply, bolt in a new D17 LX engine, keep your current harness, ECU, and then decide if you want to keep your transmission or buy an 2001-2005 HX transmission for its taller gearing. A 2001-2005 HX trans will bolt right onto your "new" 2001-2005 LX engine.
BTW, I compiled as rigorously as possible a variety of transmission specs for these cars:
http://ecomodder.com/forum/showthrea...tml#post378478
Welcome to "the fold."
james