You are on the right track. I had a 98' 700. SLP head, SLP Y pipe and pipe, MBRP can, Boyessen Rad Valves and the machine ran awesome. very reliable and stomped most of the other sleds I was riding with. Brings back a lot of good memories.
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Porting and Polishing is a whole other thing. A mild port job by someone who knows what they are doing and has tried and trued there port timing would be beneficial. If port timing is radically changed it will make the engine very temperamental, not reliable. Polishing of the exhaust port and boost ports is a good thing even on a stock ported engine. Polishing of the intake and transfer ports I do not recommend (my opinion). By polishing those ports the atomized air/fuel charge will try to come out of its atomized state as it passes by and stick to the polished ports as droplets.
You will still have to replace the Stator. The stator for Perc will have two pulse or trigger coils. One triggers forward operation and one triggers reverse operation.
I believe this statement is wrong for at least the 2003-2006 600 cc PERC sleds. They use the same stator a 19 degree flywheel instead of the 14 degree and all the magic happens in the CDI;as the stator is the same single trigger coil stator as the pre-PERC sleds. At least for the 600's; the 700's and 800's may indeed use two. I know the newer CFI sleds run two trigger coils for Reverse magic.
As for your original question; With complete IQR's now selling for $2000 and up what is stopping you from just updating to a complete newer sled? Part the Gen II out, and reuse what you want, But know that part of what makes the PRO better than the IQ's and earlier chassis is the subtle changes over the years. So if you start bolting in 90's parts it will ride like a 90's sled. If you want to take advantage of the newer technology you need to incorporate those evolutionary steps in your build. You can get the newer stuff without spending a fortune if you watch E-bay, CL, SW, BCR, and other places for good value deals. Good luck with whatever you decide!
I'm aware that the IQR won't come close to the Pro chassis in terms of handling. However, I have been paying attention to the differences in the skid geometry that the pro has vs the IQ Raw chassis, as well as the narrower front end. The only thing I really won't be able to do is mount the engine in the IQR lower then it's existing place. I'm sure the Pro has different engine mounting when you compare the two. But there's also a part that will enable you to run the 36"(?) pro front end. So theoretically I could come up with a fairly capable chassis and sled. I'm sure it won't come close to a pro, but I have always liked the way these things look, and I like the idea of having a sweet mod sled.
I have seen some of these IQR's for $2000 to $3000 which really isn't bad when I'm sure i'm looking at spending more then that to do the swap. However there are things/mods about the ones that I've seen that I would do differently.