I encountered the same issue when I dropped the transmission a while back. Jack was limiting factor on the lift - stands had plenty of room. Since I was only doing the Z1 CSCEK I was able to just slide the trans back down the tunnel a bit for enough room to work. I have decided I'll get another jack so I can remove it completely when I do the full clutch replacement.
I got the Torque Solution from Joe for transmission mount and CJM engine mounts.
TBD on the engine mount install. I'll have enough stuff out like you I think I might be able to do with with just a hoist. But I'm planning to have a shop tear open the engine anyway for galley gaskets and oil pump gears, so I'm thinking it may be easiest to do them then.