Yeah it will not go in with the manifolds on. I did not remove my battery box either.
Leaving the drivers side acc. mounts off just gave me more room to maneuver around the steering gearbox.
I see you removed the front crash bar, I did not and I could not get the motor down and in with the hoist chained front and back. I ended up using my atv lift and supporting the transmission and removed the rear hoist chain and then just rolled it back into position then lowered it all the way into place after installing the exhaust manifolds.
You probably already have a good idea as to how to go about getting it in. I am just throwing things out that I remember to maybe help out if possible.
2007 JKU X, 6.0 ls and 6L80e with a diy kit from RpmExtreme, 4.10, 4" ProComp Stage 1 lift, AEV drop brackets, 325/65R18 Nitto Terra Grapplers, Eagle Offroad Alloys 18"x10"