The 331 kit will not clear the block. No biggie though. Just clearance the block (notch) and you're set.
Just a side note, you may want to buy a short block assembly from DSS as it is more cost effective than doing the work yourself...I've 'been there, done that'.
Manual tranny and aluminum flywheel work just fine. No issues here.
DSS has a good rep. That's where I got my kit from (w/Probe SRS pistons).
Go with a Canton 7 qt. Extra oil, great pan, and looks cool too!
E