Something doesn't make sense here. The RD should have picked up the slack unless your chain was already way too long. Think of it this way -- the RD has to be able to deal with your smallest cog, so reducing the size of your largest ones should have no effect on performance.

I'm a firm believer in not counting links for purposes of sizing -- just size as if you were putting on the chain for the first time. ColinL: this guy's riding a trike with a triple up front and I'm not sure what the back.

Ramwing, the best way to size your chain is probably to put the gears in the big ring biggest cog combo with the chain skipping the RD and then adding one more full link.