Thats odd, I cant see it being that different that you'd have to make alterations to your headers, they must have pretty close to your Th350 as well, can you heat them up and bend them out the way?
I hate you have to cut the collectors, that sux.
Whatever you have to do to make it fit or work, do it.
You'll be pleased with the powerglide and never go back to a 3 speed again, that I can assure you.
They are faster, more consistent, more reliable and easier on parts than any 3 speed ever thought about being.
I see you purchased a T/S unit, good move they build some good ones and they stand behind them all the way.
Let us know how it does.
Goodluck> Cp