Hopefully you did some thorough measuring to verify that the MII front end was installed square before you plunked down your dough. If you didn't, do it now before spending anymore time on a chassis that may be messed up. Your sentence structure doesn't make it clear. Are you saying you're going to rear clip the Ford with the Cutlass rear frame section? If so, you need to do some measuring; first to see if the current rear, with tires and wheels is too wide. Since you're already narrowed on the rear, that can be adjusted with different offset wheels. The frame rails are a different matter. It's likely the Cutlass rails are quite a bit further apart than the Ford's. It's going to depend on how the existing prostreet mods were done. If they're close you might be able to massage the Cutlass rails, maybe with pie cutting and gussets. If they're quite a ways off making a new rear section out of box tubing might actually be less work, and be better in the long run.

If you were a good friend of mine I'd probably try to talk you out of it. People always tell you to do whatever you want with your car despite "what other people say". Fine enough. Of course, they're spending YOUR money when they say that. My belief is that no matter what dreams you have today, some day you'll want, or need, to sell the car. Pro street has limited appeal in the marketplace, especially on cars older than the mid '50's. You'll likely take a bigger financial hit on a prostreeted '46 Ford than you would otherwise. But hey, if you don't care about that then go for it.