I want to test out some new primers, but I know from past PCRs that at least one of my reagents is contaminated. I'm on a time crunch to finish my project and am not sure if I can get new reagents in time. Would it be ok to run PCR using these contaminated reagents and subtract the band intensity of the control from the samples for my data?

Also, will my DNA ladder be fainter as I near the end of the tube. My DNA ladder is almost used up and the smaller bands (100-200 bp) are very faint as compared to other bands (not including the 500 and 1000 markers).