Engine replacement

520i 1999
154k miles
Manual
2 wheel drive
I drove through water which cut the engine. When it restarted it made a loud bang and gave off white smoke (injested water). Car ran afterwards but with constant ticking sound. Started usuing more and more oil and increasingly fired on only 5 cylinders. Last Sunday the engine went bang! Big end bearing on cylinder 6 let go and smashed out through engine block. I have bought a used engine with only 38k. I ahve started stripping old engine down in car ready for swap over. Though fiddly I have finished everything in the engine bay.
My problem is this - the exhaust manifold bolts and the gearbox bellhousing bolts are proving impossible to undo. Anybody have nay tips?
Thank you. Glenn