It's difficult to say what is actually happening, here, without knowing the condition of the parts being used.
I agree that it seems like the spool mount rubber is trashy, combined with loose manufacturing tolerances from Headman. I'm willing to bet that you've lost a lot of height on the left side mount. Usually, you don't see spool mounts break clean off and let go like the disc mounts do, but when they go, they get really loose and the weight of the engine sags them, especially on the left side, because that is the side that wants to lift and come back down. There is more movement coming from the left side, from engine torque.
These work great;
http://www.summitracing.com/parts/ens-5-1106g/overview/make/dodge
I wouldn't mess with the transmission mount. If you do that enough to move the header away from touching the bottom of the torsion bar, you'll risk screwing with pinion angle, even more if you do replace the engine mounts.
Right now, the reason your engine is cockeyed and you want to compensate by lowering everything, is because of the left mount.
You'll need to keep the engine up with some wood under the pan or an engine hoist and a propane torch to remove the old rubber from your mounts, to slide the 3 piece units in, if you go that route. Pretty basic install. Sometimes the ears on the K member will need some persuasion. A long bolt and stacked washers with a couple of nuts will work good as an expansion tool. When they installed the mounts from the factory, that spool eyelet bolt crushes the ears on the K member a little bit. The old ones will come out, no prob, but the new ones will need corrected/ expanded K member ears to go back into.
It's worth the $35. They will keep the engine from moving and further risking header contact with the car, causing header gasket/ seal damage. It may not be a bad idea to pick up a trans mount as well, depending on how much HP you've got.
