I was adjusting my rockers the other day with the intake off and went by the adjusting order my haynes manual stated. However I noticed that there were a couple lifters that were raised up. Obviously they weren't on the base circle of the cam which you want when adjusting them. Could this be because of the increased duration of the cam? If so what kind of problems would it cause?

 

Yes,
The rockers were on the ramp side of the lobe. I always lash in order, starting with #1 at TDC. You will know when #1 is at TDC when the #6 exhaust valve comes up and the intake valve just starts to move down. Then you set #8 when #5 "rocks", then set #4 when #7 rocks, #3 when #2 rocks, #6 when #1 rocks, #5 when 8 rocks, 7 when 4 rocks, 2 when 3 rocks. I set mine at zero (pushrod just spins between your fingers) and then another 1/8th turn. Once you have a few miles on the car, its best to set them when the engine is running.