I removed the engine yesterday evening, I was hoping to use the chains and a load leveller. But the hooks on the engine are tiny (2.25 diesel), so I just put a rope around the whole thing and did it that way.

Ideally though I'd like to use the leveller when putting it back in as I can get the angles just right. Could I bolt the engine hooks to the chain, or even better would a small D-shackle take the weight?

Shackles would be fine, they have the wieght marked on them.
8mm should be OK, 10mm are rated at 1 ton. As a guide use the same shakle dia as the chain or one size bigger

Great, thanks, I'll get the largest size that fits through the lifting eyes.