For those out there who have been lucky enough to obtain a box or two of Phase 2 clones, apart from the helmets is there much difference between the P1 and P2 models? I'm just trying to see If I can 3D print some P2 helmets and stick them on the bodies of the P1 clones from the core set in order to provide some more variety with poses etc.

Yes you can.

The only difference is the pose, the helmet and the weapons.

There may be a couple of those shoulder pads

I used the parts from a core set and the Phase 2 to make two full units with one phase two box

The P2s helmets can be used with P1 Clone bodies with some slight modifications, I did it for one of my Z6s. The main issue with the Phase 2s in my mind is that they are in very fixed poses so you can't say swap the arms around to make them different, at best you could build the Phase 2 heavies as standard clones rather than with their heavy options.

Phase 2's have pretty static poses on the hard plastic sprues. The main differences are that you get more options with the heavy weapons poses- you can assemble the Z6 guy without the Z6, or the mortar guy with mortar deployed or on his back. I think the phase 1's have more customization overall in that you can swap arms between most of them to create different poses.

I originally didn't think I would use the Z6 so I built my guys without them, but later clipped the hands off of the Z6 itself and glued it to their packs, hopefully a bit different than most people's Z6's.

There is plenty you can do

I turned 3 units of Phase IIs into 5 by mixing in Phase Is and Phase I Trooper Upgrade minis, along with 3D printed Phase II helmets. The three Courscant Guard squad leaders are all different sculpts/poses because of this.