the only issue with fitting a larger bore is it can lower back pressure/compression (and for more power without a turbo you want more compression..look at tuning a 2.0 8v and you'll see loads of higher compression pistons etc..and boost increases compression, hence for big bhp on turbo's you need low compression pistons/head gasket spacers etc..a mate has an evo with a 12mm head gasket so he can run silly boost with loads of lag!)
A vr6 exhaust won't really make that much difference although you'll possibly/maybe notice it needs a few more rev's and have a narrower power band (which on a 1.6 won't really matter!!) I had a rover 1.8k before that when de-catted and with a larger exhaust it lost 5bhp and 14lb/ft of torque and was flat until 3500+ rpm!!
