A 1" difference is not unreasonable when trying to level ride height, however, it is not ideal. It is recommended to set the spring perches within 1/2" of another to avoid negative impacts on corner balance and handling.

There are three things to consider here:

1: These cars (pretty much every 79-04 Mustang) will naturally lean to one side, usually the driver side. This is primarily due to the extra weight on that corner. You have the battery, brake booster, power steering pump, fuse box, steering shaft and column, and driver seat located on that side of the car. All that extra weight, combined with a flimsy unibody chassis and the driver getting in and out of the car over the years, will induce a lean. Basically, you can adjust the spring perches all day long but one side will almost always sit lower/higher.

2: Ride height adjustments to one individual corner will affect the other three corners of the car. Raise one side the other side comes up, lower one side the other side goes down. Same for front-to-back.

3: Measuring from the ground to the fender is not an accurate determinate of ride height. The car should be parked on a level surface, and the distance from the control arm pivot bolts to the ground is measured.

I went through this on my car. I would adjust the spring perches and lower the car and everything looked level, but after driving around the lean would come back. I gave up on trying to get it perfect, so I set the driver side front perch 1/4" higher than the passenger side front. Rear perches set the same. I've found a happy medium with those settings.

 

Ride height is ultimately irrelevant to properly setup coilovers. Get the ride height to the "area" you want the car to sit in and then get the car corner balanced. Corner balance the car to have a 50/50 CROSS weight with you in the driver seat or equal weight. The cross weights being Driver Rear to Pass Front and Pass Rear to Driver Front. Driver side to Pasenger side weight distribution doesn't matter, just the cross weights.

From there, any adjustments to ride height should be made equally to both sides to maintain the cross weights. If the cross weights are good the car should sit correctly. The overall distance between the various spring seats compared to each other is also irrelevant. The only time it would be relevant is if the shocks/suspension were bottoming out on one side of the car or one corner of the car.

 

Cool,thanks for the info guys. It's not a race car so I'm not overly concerned with having it perfectly balanced or having the absolute best height adjustment. Just want the car level from the passenger to driver side and a slight forward rake. It has settled some and right now the driver side is lower so I'll keep playing with it.