I got my car all back together after rebuilding the suspension on my car. Once i had the car lowered, I drove it around the block to get the suspension settled. After, I went back and measured the ride height of the car. I installed Moog 5662/5665 springs. The fronts had 1/4 coil cut off, the rear 1/2 spring. My ride height measured

LF 27 5/8" RF 28 1/4"
LR 28 1/2 RR 29 1/4"

I'm going to trim the springs a little again to get the ride height where I want. What I would like to know is how much of an impact does the front spring indexing have on ride height. The LF spring is near the middle of the two holes, close to the 2nd hole. The RF spring is only covering the first hole about 3/4 of the way. Would this difference between the two springs account for the difference in ride height between the front sides?

there would be a difference, but not much between your current setup.

Also, dont measure height from the ground either. If its not perfectly level, the measurements will be off. If you have different wear, or different tire pressure, your measurements will be different as well. Your better measuring from the wheel to the fender

What would you do to do that maybe hold a level on the edge of the rim?

no, clip the end of the tape measure to the bottom lip of the wheel, and up the to the fender. simple really

All right thanks for the information, seems like the more projects I finish on my car there are always two more to do.