This is probably a wierd way to go about it, but here is how I did it. The stock swingarm and lower mounts on the CR250 fit the 500 engine as they sit. I set the engine ih the chassis and cut out the stock clam-shell "Y" where needed. I make a wooden dummy "Y" section that I could push into place in the frame. Checked all the clearances, mocked up all the hardware that may interfere, and removed engine a few times to be sure it was serviceable with my proposed "Y" section in place. Once that was done, I carefully measured my wooden dummy and duplicated it by machining a billet unit that extends into the original downtube 1/2" . The rest was pretty straight forward. The pics tell the tale.
I know a lot of people do not like the idea of welding a billett piece the the tubular frame, but it seemed the best way to do it for me. I know SH did it for some years, so I went with it. No problems to date either. I had everything professionally welded and they assured me that I would break other factory welds before this would go south. Feel free to contact me if you would like more pics or advice/opinions. Thanks