I plan to do some changes, does anyone know if a cap that woudl fit on the header where the EGR tube goes is available? if so, what size and where did you get it.

 

I think it's 3/4 with garden hose threads......... no kidding. You should be able to find a nice heavy duty brass cap screw at your local plumbing supply house.
Bring your EGR tube with you to double check to make sure threads are correct and it's gonna fit properly. Get one that you can put a wrench or socket on........ (not one of the little hand twist on ones that you would use on your garden hose)