It's because the manifold is not only physically taller and thicker, but longer too. Plus you're adding the adapter to it. So to answer:
1. Will the 4
bolt LS throttle bodies line up with the L26
intake bolts? -
Yes; however it's a totally different setup (cable vs. DBW). Won't work.
2. Is a LS1 Maf even tunable for a n/a basically stock engine? Would it go that low?
Tuneable; sure. Worth it? Newp. Told ya that already.
3. Is there any other options other than of course cutting the hole out or going back to L36 manifold? Sure. Plenty of options.
Sell the Trasher Intake and just go to an open cone. It's an N/A 3800. You're not making any difference in power...and if you are, you aren't noticing anything.