really don't want to be the bearer of bad news .... but you might as well get used to the cut it off and re-do it part of modding these things.
When i converted my 3203 to the 150/swingarm, I ran into the exact same deal. i thought i was smart and laid it all out, chopped up the frame and made a "window" for the engine.
thought it came out pretty nicely ....
put it all together and found the swingarm hit one of the tubes--had more travel than i expected ...
chopped out and moved a tube
and found the carb hit the rack then ... chopped out the rack
and then found out .... you get the pic...
throughout all that i went through 2 shock length variations and about 3 or 4 different upper and lower shock locations and two different size shocks.
now with the IRS, i had to chop up that same tubing i moved twice yet again ....
best to get into a tack it and test it mode to reduce the cutting/grinding work if it doesn't pan out.
Is there any way you can set the engine back further on the swingarm?
There's also the idea of making a set of dropped and extended swingarm mounts.
one final thought --- and i doubt you'll go for it, but i'd love to see someone do it ... set the swingarm up with limited travel--2-3 inch range--run and engine like you have to a fixed center sprocket carrier and run lower a-arms and sliding u-joint shaft with another short stroke shock set.