Is there a main difference between the L36 and the L67 engine, besides the supercharger?

Compression ratio is different, the L67 uses forged pistons and crank, the cam gear is different, the heads are different, the lower intake is different......about the only things that are the same as in IDENTICAL, are the TB, the valve covers, and the block itself....maybe the exhaust manifolds also, but I'm not positive on this. Jr or Hector would know, and I might have missed a couple things. Where your REALLY get into some differences is between the L27 and L36, also. They're not as closely related as they may appear, either.

If the same supercharger from the L67 is put on the L36, will there be some conflicts then?

Yes there will be conflicts. The injectors are also in different places on the L67 and L36. That'* why the L67 has then in the heads and the L36 has it in the manifold. The exhaust manifolds are the same for all Series II engines so when you put headers on an L67 that'* why they gain 20HP to the wheels easy. The Series I (L27) and Series II (L36) N/A engines are really different. A swap between the two would require quite a few items. Including the Series II exhaust manifolds since both engines have different heads.

I posted an article on this subject up in Techinfo.
Here'* the link:
http://www.bonnevilleclub.com/techinfo/?article=43