Right that seams a sensible idea tom and most economic in terms of budget, the tunnel changes can come at a later date when its a complete shell again, there are a few differences on the front subframe like the rear mounts and the top tower mounts which are twin bolt, the front bulkhead crossmember construction is different although you wouldn't notice from the outside, all the inner support around the towers are different (these parts are available from M-machine also).
When you cut the mk4 floor out make sure you leave plenty of metal on to trim and drill spot welds out later when you can see it properly, best bet might be to draw lines were you thinks best to cut it and post pictures up in this thread or your project thread so we can see if you're about to cut i vital area out or not haha