I'm using a pre-89 7M shroud with a 2JZ clutch and fan. I have it setup with a factory 7m radiator, and the clearances are very tight even with the thin factory rad. Actually I had to modify the stock hold downs so that I could pull the radiator back a little bit more away from the fan, because it would hit under braking.
I really don't think it's going to work out too well with the big Koyo, Aaron from DM was talking about using a clutch from an LS400, and a stock 7M turbo fan, to get the most fan to shroud/radiator clearance.
As far as it not lining up, I'm lost there. I've had my factory shroud on 3 different radiators, and it's lined up on all of them fine. You might have to make brackets for it to bolt to the Koyo on the bottom. On the stock setup it has little slots it slides into on the bottom.