Would I need to increase the jet size to go with that though? I've got a set of 112s to go in the 'new' carbs as that's what's been recommended to go with the Scorpion can rather than (in theory) the stock 108s that it will be running assuming I don't find the previous owner didn't rejet to suit.

I think it would run like shit on standard jets

That's what I figured, but I was wondering if going up to 112 to account for the pipe as per the jetting thread elsewhere would help to compensate for that, or if I'd have to go a bit bigger?

You wont need to go any higher than 112 for fitting a k&n, 110 would probably be enough for just an end can and k&n.