YAY! Another Mk3 Jetta 2.0! I am no longer alone! WOOHOO!

Okay. Haha.
It doesn't look too bad. I'd just stick with your plans to remove the loom and interior bits, but I would leave the engine mods alone. For the shift knob and boot, you can get a Mk4 shift knob & boot to replace the Mk3 one. The Mk4 knob and boot look much better. As for the pedals, you should be able to get Audi TT styled pedals (the brushed metal look ones) that fit perfectly for around $90. I would paint the air ducts, repaint the side trim (it looks kinda funny in the pics), get a Euro VR6 front lip (like $100, can be found on just about any VW enthusiast site), and get a badgeless front grill. If you need to know something about the car, ask me. I have official VW shop manuals, a Bentley repair manual, and several other repair guides for the Mk3s.