I put some side pipes on today and one side (passenger) is low..seams normal, but the drivers side is rubbing on the bottom of the body pretty hard. Do I need to shim the passenger side mount? has anyone else had this issue?

You might need new motor mounts.  Are they oil soaked or broken?  

the mounts are brand new solid mounts

side difference

You may need to trim the lower fender. See this for installation: http://willcoxcorvette.com/instructions/side_exhaust_install_guide_1969-1982.pdf

good to know, but should it be off this much?

Hmmm.....first question....Are you using the factory exhaust manifolds?If so, is the heat riser still on the passenger side?
It's hard to really tell from the pics how much difference there is, since the pass side pic is taken from below level, and the driver side is from above level, but it's obvious there is a large discrepancy. If you have the stock manifolds and the hear riser on the passenger side, that could explain the difference in clearance.
Most sidepipes like that do tend to hug the body pretty tight, and may even touch...just depends on the manufacturer. Imho, there is too much difference for this to be engine mount related. If it was that low on the passenger side(due to an engine mount issue), it seems like the dang fan would be clipping the fan shroud, and the steering linkage might be rubbing on the oil pan.
This looks to me more like just a set of pipes that are not bent/welded properly for the car. You can trim a little of the body off where the pipes are hitting, but will the rocker panel trim fit?
Most of the Mid Year Corvettes with sidewinders had to have the body cut right in that area from the factory for the pipes to clear. Don't know that I've ever heard about the same issue with the '69s, since they were the only Shark cars to come with factory sidepipes.
You might just need a torch, and stand on the pipe to get it to clear on the driver side, and maybe a little body trimming. The passengers side looks like there is way too much clearance on it....may be able to heat that side and jack it up a little closer. Just remember, even tho you have solid engine mounts, the engine is still gunna torque UP on the driver side, and down on the pass side.
hth

The pipes are headers, not stock and I posted a while ago about the fan being too close to

Not that I am aware of. THe only thing I could suggest would be to remove the carb, and set a level across the intake. The problem with that is, you would need to determine if the car itself was level....and I got no idea of how you could do that.
Ida know....you may try sticking a couple of flat washers between the mount and engine block on the pass side, and see if that makes the difference. I remember someone here stating that the solid mounts they used were different left/right....maybe yours are too?
Is there a chance that the frame might be a little tweeked on the car?

I read somewhere too,  to put a level across the intake which I did and the engine is listing