1) Before manual installation provide proper writable permissions to directories(refer install.php or pre-install steps on loaded7 site).
2) For manual installation install twice i.e. with SSL and without SSL. and check for difference in each installed files and SQL.
3) Install with sample data.
4) Please create function to check required PHP Settings of enduser PHP binary.
5) Choose Database type : MySQL-InnoDB(Transaction-Safe)
6) Move images/ images to package and make zip.