4.6 into 4.0 car

Just out of curiosity really, but I may have found a 4.6 engine for a good price, but I have the 4.0 in my range. how easy/hard is it to replace the 4.0 for a 4.6. Could i just replace the bits I need (short block) or is it better to just replace the whole engine?

Secondly, I have an LPG system; I know nothing about LPG. are they set up for specific engine sizes? can you 'recalibrate' them, etc?

No reason why the 4.6 won't fit and I would replace the whole thing. Obviously there are two types of engine, the earlier GEMS with the box type plenum with either 4.0 or 4.6 cast into the top and the later Motronic THOR which does not have the box but sweeping pipes and you should change yours with the correct type. The blocks however are the same.
The inlet manifold on yours has been tapped to accept the gas injectors, unless you are getting a LPG engine, you will either have to swap the manifolds over or drill & tap (M6) the other one. The system should be sequential and self teaching as electronically it works on a closed loop system and is self tuning.

Mine would be the gems engine then with the 4.0 on the top. Does that mean I should stick with another gems engine then?
I'll keep the manifolds from my engine and swap them over for the LPG system. Seems easier using one thats been done then messing about trying to get another right...

It would make more sense to use a 4.6 gems in your car as it is physically a direct swop,wheras a Thor engine would fit but you would have alot of parts to swap over including changing the cam sprocket.
You ought to use a 4.6 Gems ECU aswell,they run a different fuel/ignition map to the 4.0.
The LPG system would be OK but would need recalibrating via its own software to fuel the bigger engine,and then fine tuning with either Testbook or Autologic etc along side to ensure the fuel trims stay within what Gems would try to be doing.This will avoid the long term fuel trims being so far out that the car only ends up running ,(Semi) properly on one fuel.