If your gearshift are rough, that may be a clue as to how the chainring (and most likely just the teeth) are bent out of shape. It sounds like you need to go back to square one, and look particularly at how the chainline is when the chain is on the middle chainring, and on the fifth cog on the rear. If there is a kink in the chainline, you have a problem. Did you change the BB cartridge for a new one of different spindle length when you undertook the project?
You may also need to look at your riding style... do you ease the pressure on the pedals (but not pedalling of course) when you make you shifts?