The deck height changes the position of the cams and therefore cas. When you lift or lower the head, the cams have to rotate to maintain the same belt length on the drive side (imagine doing that with the tensioner loose, it makes more sense.)
I seriously doubt an rb30 block works out perfectly the right extra deck height to work wit the belt. it is very close, but slightly different so will need adjustment.
disconnect tps on a neo to put it ibto base timing mode, not sure pre neo.
Dont know why the loop sucks, but it does. a normal plug lead will work between the coil and will be accurate.