One side went in just fine, but the other side's bolt hangs about 2cm too close to the front of the vehicle. Managed to get it over halfway to the hole using the weight of the dropping engine to leverage it back. Tomorrow going to jack up the back of the car and take the jackstands off the front sides with the front jacked up slightly for crawling space, see if that helps the engine settle in tomorrow. Has anyone ever run into this problem? There's nowhere good to get a crowbar on the frame and engine (steel) with the timing belt cover on the front it seems

You've undone the 2x bolts that hold the top of the gearbox, the pitch stop ?

The engine is hanging correctly & should be on a suitable engine hoist ?

& the mounts are good?

If that's a yes to all, then you should just be able to give it a wiggle n' push with your hands and it'll go in smoothly both sides as you lower it.  No crowbar normally is needed.