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 The 331 you might get away with free and clear.  For my 347, I had to notch the lower cylinder walls for my rod bolts.  If you are really concerned talk to a tech at DSS.  I would recommend a 7 qt. pan and a high-flow pump as well.  Its always better to be safe than sorry.  As far as the flywheel, aluminum would probably be fine.  I personally would get a steel one though cause their just a little stronger. 
				__________________92 Mustang GT, 347 Stroker(Forged Steel Crank/Rods-Balanced, Forged Aluminum Dished Pistons), Trick Flow Track Heat Intake, Trick Flow Twisted Wedge Heads w/ Stage 3 port/polish, 80mm C&L MAF, FMS 30# Inj., BBK AFPR, Trick Flow Stage 2 Cam, Trick Flow 1.6R Rockers, BBK E.L. Headers, Flowmaster Cat-Back, MAC CAI, FMS Pulleys, Griffin Alum. Radiator, MSD Pro-Billet Distributor; AOD, Dynamic 3300 Lockup Converter, B & M Super Cooler, B&M Ratchet Shifter; 3:73 gears.
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