looking to buy a reconditioned engine from a skyline will my vl gear box go onto a r31 rb30 engine

Yes

It there any difference between a r31 block and head and a Holden one?

apparently some of the plugs are different, no first hand experience though

most of the ancilliaries are different, distributor, alternator etc but the block and heads are the same.

I put a vl engine in a r31 and some small differences annoyed me like the heater hoses were different sizes so it took ages to jam them on the vl block as the skyline ones were tiny. Apart from that I just used everything else from the skyline(flywheel, altenator and bracket, sensors, loom, manifolds, power steer pump, ac comp,rocker cover, engine mounts and computer and it ran like factory.