noticed today after fitting some second hand carbs that one of the headers is cold, any help on what i should look for would be great

Carbs need balancing then. Guarantee one cylinder is running way too lean.

Yea Im trying to balance them now but it's not doing much first time at trying though, I've set all the pilot jets to 2 1/2 turns out and it's up to temp but the 3 of the gauges seem to just sit in the red bit that says late valve timing or leak at intake and the don't really move when you adjust them, so I'm kinda stumped

Right i've taken a photo and a video of what its doing or not doing, I've tried to adjust the carbs but it makes no difference on the gauges at all
http://s4.photobucket.com/albums/y136/B ... gnal/Help/
I'm tempted to take the carbs back off and check the float hight and blow out all the jets

also does it matter where the long or short vacuum pipes that screw into the inlet go as i had to put one of the long ones on the out side cylinder as there was no way it was going to fit on the inside cylinder

Have you cleaned the new carbs? Or just stuck them straight on?
Cold header on my 29 was blocked air intakes under the plastic cover that secures the intake trumpets to the carbs. Soaking in carb cleaner over night and blowing through with compressed air cured it.

I've taken them back off and checked all the float heights and blown all the jets out with a air line also decided to check the plugs and found the one with the cold header is going down, had a weak spark and was damp, cleaned it up and was the same then it stopped sparking so going to get some new plugs then refit the carbs and go from there.