It will fine - don't worry so much :)
If you stretch the holes down then you need to fill up the holes above

I'd only do it to get the caliper so it fits then use it as a pattern. I doubt the bosses that space the hub / swingarm and caliper centre / swingarm will remain the same so it will need to be remade anyway.

In the back of my mind, something tells me you would have a much much easier job making this/these fit:
http://cgi.ebay.co.uk/Yamaha-XJR-400-Wh ... 19c475904c
Not certain about that but believe it to be true.
150/60-17 rear tyre, use your original disc, and have it matching the existing 3-spoke wheel. I was thinking about / looking into fitting one of these to my 600 Divvy but in the end settled for a FZR600 wheel that was still 18" but at least took a 150 instead of a 130 and was a straight bolt-on fit.

My bike's a 3TJ, it alreay has 17" wheels - the wheels I'm trying to fit are Dymag TT3's. The rear Dymag has a 1/2" wider rim but I reckon it will go in, somebody has fitted up a T'Cat wheel and they're 5".


FZR400RR 3TJ yesterday