Ok so my heads recommend a comp 7949-16 (.100-inch longer than than stock) in the instructions but when they installed them they used 7940-16 (stock length) Could this be causing it not to put out the power that it should?

 

It might.
It will cause early guide wear,depending how far they are off.
Recommended length is not always correct.The length should be checked with an adjustable pushrod and a solid lifter to get the pattern on the stem right,then measured and that's the ordering length.

 

so you think i should just get new ones that are measured then? would it be hard to do?

 

YOU need to measure YOUR engine and get the right length.
The one's ya have might be right,who knows until ya measure.