1. As far as I have learned from a lot of reading and some (O.K. not much, but some) experience, the 1.7L (90mm) through 2.2L (96mm) are a direct fit into the "spigot" hole of any type-4 case. It is the head on a 1.7L that needs to be machined to accept anything over a 1.7L designed P/C. That said I think there are still some 96mm 1.7L big bore kits made by someone (markstephenshp.com I think) so that may be the way to go. Otherwise 1.8L (93mm stock) or 1.8 big bore kits could be used with a modification to the head. However 2.0L (94mm stock) and 2.0L BB kits CAN NOT be used with a 1.7L or 1.8L crank and rods. The wrist pin is located for a different stroke. To fit the 100mm-104mm P/C's you probably need to machine the case and the heads. Cranks are O.K. until 76-78mm then internal clearences get tight, the rods and internal structure of the case need to be machined.
2. If you increase displacement it is neccesary to increase valve size and ports to take advantage of the cc's. Volumetric effeciency of an engine is a system, approach it likewise. From what I've read the D-Jet was designed fairly well, there weren't the emmisions/MPG issues that killed cars in the 70-80's (retarded ignition timing, retarded cams, lower compression...) so if you go much beyond the stock displacement (2.3L+) look at boreing out the throttle body, bigger injectors, ported heads, etc.
3. Lightened FW's simply remove rotating mass. Good because it lets the engine rev up quicker, bad because it lets the engine rev down quicker. Some people love it, but it does change driveability, maybe it is offset by the extra hp? Ask Ian if you can test drive his car
4. People argue about cams all the time, the stock one is pretty good. The modified cams don't offer much except to move things around, more top end-less low end, a lot of top end-no low end.
What ever you do, figure out from the beginning a plan, a timtable, and a budget. Following what someone else (like Ian) has done with success is a good idea. Or talk to an engine builder (FATS, Mark Stephens). If you want to keep the D-JET with a highly modified motor it will cost money, see if an aftermarket FI is cheaper in the long run.