Is it a "heavy" knock? Or more of a loud sharp hammer tap~tap~tap? I'm asking because an exhaust leak at the header pipes can sound like that, more so because you say it goes away when it warms up, a small leak like that will close up sometimes when it warms up. hopefully that's all your looking at, let us know what you find?
From what I've read & heard sometimes when the headers are removed for whatever reason, some less experienced wrenches forget to pull the old copper seals out of the exhaust port.
I've heard guys finding two..and three gaskets in there all squished together.
To find out if it is a rod bearing you could dissconect one spark plug wire then start the bike if the noise is there shut if off connect that plug wire and go on to the next if the noise does not go away or get much quieter on any of the cylinders you test the problem shouldn't be the bottom end. Before you cause further damage may I suggest refrain from running it untill you pin point the noise.
Have you checked the oil pressure with a gauge? A good compression test wouldn't hurt things either it's nice to know the condition of the engine your working with. The more info you get now may help you decide which way is best to repair it.
What's the mileage on the bike? Rod or main bearings have a fairly distinctive sound when they're done too. Lower the pitch of the knock, usually the bigger the extent of damage Remember the 1200has hydraulic lash adjustment, but I have no experience with them being bad so can't say what to listen for. Stethascope may help.