You'd definetly find it much easier to bolt the gearbox and the engine together out of the car.
Do yourself the service of doing some tidying up in the engine bay whilst it's got no engine in it, that's one thing you learn with being part of an engine conversion
When we were doing mine we pulled the Neo out of the halfcut with the loom still on it (Had no reason to take it off), the only thing we did with it was feed it through the firewall for when the electrician went to wire it up, so I can't really offer much insight as to the connections on the engine itself sorry.
Just looking at the engines side by side you can see a few obvious differences. If you still have the RB25 originally from your R33 I'd plonk the engines side by side and just look at them & pick the differences, preferably with an R33 and an R34 service manual at your side