Engine reassembly order
 

I'm just about to start reassembing my motor and putting it back in my bike.

Which do you recommend I do first? Reassemble and install? or put the engine case in and then put the cylinder and head back on?

When I have any engine out of a vehicle, and I can do all the assembly out of the vehicle without any vehicle fitment issues later, I do all the assembly with the engine on the bench or in a stand. You run less risk of dirt and parts dropping in critical parts of the engine and don't have to fight parts of the vehicle when installing major components of the engine. I wouldn't pull the engine to do a big bore kit, but if the engine was out, I'd do pretty much everything but the carb outside the frame if possible.

If you have trouble securing the engine to work on outside the bike, get some 2X6's or bigger to construct a simple, makeshift box or engine holder. Now, you might find it easier to torque the really heavy bolts on the crank gear, flywheel gear, and clutch basket gear with the engine in the bike, but a good wooden box holder can secure the motor quite well.

I just had to replace my crankcase. I rebuilt the entire engine on my workbench, and then installed it in the bike. I clamped mine gently in a vise to hold it while i worked on it. TNC's box jig would be a good way to do it too.

Thanks guys - ever fire it up on the bench for testing?

Being a liquid cooled engine bench testing would not be worth the effort.
I have bench (floor) tested air-cooled VW engines prior to installing them into the vehhicle.

I have only ever done engine tear-downs & build-ups with it OUT of the bike and can't imagine doing it any other way.

I once did fire up an XS650 engine on the floor. It was a time-consuming to get the fuel & electrics connected properly (ol'klx is right, water cooling would add another whole dimension of complexity) and even with a 2x4 cradle, it shook itself all over the place once it was running. I wouldn't bother doing it again. Just give the reassembled engine a few turns over by hand to be sure it spins ok, then get it back in the bike before firing it up.