"I've been hearing a creaking sound coming from the crank lately, it just popped up after a few weeks of riding. It sounds like metal being distressed a little, at first I thought maybe the crank arm was twising a little or the crank was bending, but I doubt that. But it's coming from the crank area and I'm hoping it's nothing serious. It usually happens when I'm doing a track stand."

Make sure to check your crank bolts. This could be causing these "creaks" and it could also be the route of your chainline problem. If the chainring side isn't tightened down enough it could cause those clicking noises in your chain. Also, what size chain/cog/chainring are you using? (1/8, 3/32) If it's a combo, that could also be a problem. Whatever you do, don't listen to 53-11. BTW, Nice conversion. Old brown frames are classy!!