Yeah most people worry about the fender lip, but as you lower the car other things definitely come up. When I was running drop spindles on my Challenger I had to remove a fender brace and then discovered the issue of the distance to the top of the inner fender. The idea of the drop spindles is you can lower the car without losing suspension travel, but it doesn't work as designed because you still run out of clearance. So you don't get to "keep" the suspension travel anyway. 72BBswinger ran into the same issue on his Dart, he wasn't using drop spindles. You can see his solution here
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The thing is that if you run larger torsion bars you don't need to keep all of that travel anyway, the larger bars will result in less suspension travel. Although honestly on my car because of the QA1 LCA's and the altered bump stop heights the suspension travel is fairly close to stock anyway. The earlier QA1 LCA's without the integrated bump stops add almost an inch of travel, and by shortening the lower bump stop on the frame I gained almost another inch. So the ~2" drop didn't change the overall travel on compression, and the taller upper bumpstop keeps the down travel similar as well. I don't need the mods that 72BBswinger did yet, but if I lowered more I would. But for a daily I'm already as low as I want to be, lower would just cause more problems.
5.5" to the header flange? That's not that far from stock ride height. Heck with as short as you tires are it might be stock. But with the drop spindles installed that means your control arm angles are actually worse than stock, effectively you've raised the suspension 2" which results in terrible geometry. Which is another reason I don't like those things. If you use them, but don't drop the car the full 2", you end up with even worse suspension geometry than factory. The camber curves and roll centers will actually be worse because of the control arm angles.
At that height you could easily be using stock spindles. If you look at your control arms you'll probably see that the ball joints are well below the attachment points with a steep angle on the control arms.
