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Since I'm building a 331 for my '65 Fairlane, I guess I should vote there. The reason I chose that was simply because the kit was on sale for $400 less than the 347 kit at the time I bought it.
I wouldn't shy away from either for a properly built engine. Just make sure the pistons you get with the 347 kit don't have the piston pins going through the oil ring as is the case with the first kits made. Newer kits don't have this problem.