440/4 speed install, which method?

Attempt 1: Well guys I worked on the Cuda over the weekend. Since the trans was already sitting in position I tried installing the engine in from the top. I got it real close, about 1/2 " between bellowing and H lock but couldn't line the shaft up so it would slide in place.
Attempt 2:
Pulled motor out, Removed Hurst shifter, removed trans. Sat trans on a milk crate, engine back on crane, checked my clutch alignment with the alignment tool. Slid the trans in. At this point I was about 1/4" gap bellhousing to block. Wiggled trans around, put in a couple of bolts and I was just on the dowls. Tightened up the bolts. It didn't go together easily.
Lifted it I'll in position and dropped the while assembly in from the top. Just cleared at max lift on my engine crane. Once trans was under, used another trolley jack under trans to level it out. Moved whole assembly back to line up my mounts and lowered her down. Spent the next few hours installing everything else and was ready to run the cam in...super relieved it was all in and excited to finally start it. Turned her over and click click click.... ******* battery. Read 12.9V but indicator on battery said recharge. That battery been sitting for a few months and I had it on charge overnight. :(

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