I would go with the Jfab rails, service honda cuts the stock set and mounts a piece to fill the gap, I don't like it. I've done 3 now and did the first like that, the second was a 250 2s and the last a 500, on the last two I bent my own rails (used a JD3 bender for square tubing) using the radiused tubing and they came out great, looked just like the Jfab rails. you really don't have much in the way of options when installing the motor, it really does have to be positioned properly, the center line of the countershaft has to be in the center line of the swing arm, if you roll the motor up the chain get loose as the suspension compress and of course as it goes the other way it gets tighter, so like the stock you have to have a compromise, and fudging one way or the other can have consequences. So don't position the motor for reasons of clearance or anything else, the clearance is what it is and you have to live with it, having said that I think my 500 has more clearance that the 450 did.
The other thing, I think Sandblaster is on to something with the duel headstays, I haven't done it yet but may.
I used a 250f for the 250 2s conversion but not the 500 conversion, for some reason, and I may be wrong, I thought there were issues with the tank hitting the motor, but don't hold me to that, was it sandblaster that said he melted a hole in his tank trying to form it or somebody else. The 250f Showa suspension bolts right up to the 450, thats what I used on my latest.
Worth the effort for sure, by the way, I also like (maybe even more) 04-05 250f steel chassis, good suspension (newer will also bolt right up) and they feel narrower than the Aluminum chassi bikes
Good luck