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If you want to do it right from the start, I would build the bottom end. Thats going to be your best bet. Other then that, make sure you have a good fuel pump (i have a Ford GT w/ KB BAP), larger injectors (39 or 42's), good spark plugs (NGK TR6), a good MAF (i have a blow-thru MAF w/ Diablo Extender) and a good tune.
If I could do my build over again, I would build the motor up first. Good luck with the install.
bruthru2003 is exactly right....however, you can build a fun DD supercharged 2v that is reliable without tearing into the bottom end....just make sure you have the supporting fuel mods and a good tune from a reliable tuner
very true. Ive had my motor right around the 400 rwhp mark on the stock bottom end for about three years now (through an auto) and the motor still runs like a top.