I seeYou want to muck about with the stoke to gain a little more swept area in the hope of getting more power and then shove a FZS400 engine in a FZR250, right?
Most gains are had by increasing the bore and shortening the stroke as Yamaha did with the YZF600 R6, going from 62 x49.6 for the YZS600 (Tcat as we know it) to 67 x 42.5 for the R6. Or decreasing the squash band, sort of increasing compression but gives you better mixing. Where as, I think you want to decrease (destroking) the stroke, to increase the swept area (by using YZF conrods/pistons or a mix of FZS parts) but that could well also lower the compression and will change the squash area? Or have I not read you right?
You make no mention of swapping the block 600 for 400?
Other than point 1 of your list, it makes no sense, the gains will be a minimal for the work and you'll more than likely have to play about with the fueling to get it to run right and produce power across the rev range. The power increase in the Tcat (15hp ish) over the FZS is all mainly in the head and intake (the block is angled forward slightly and the intakes are 90* to the ground i.e. straight down and in) plus the T cat revs faster. Basically from the crankcase up the YZF is a completely different engine. The R6 is totally different in all areas.
Unless it's all about point 1 I'd be more inclined to shove an R6 into the 250 frame now your talking, quite a bit a fabrication but it will go
What about wedging a FZS600 engine in..?
Partially correct, we're planning to basically overbore the FZR400 from 56mm to 62mm with either YZF600 or FZS600 cylinders & YZF600 cylinder head - various rod/piston combinations/choices to get compression height spot on - this may go into an FZR250 or an FZR400 - TBDthen a possible combination of cylinder block and conrod and pistons @62mm bore - fortunately there's quite a few pistons available in 62mm, because a straight swap of say YZF600 top end, with the same squish band with the reduced swept area would see compression fall from 12:1 -> 9.78:1 - not good!