There's no reason to toss what you have, and you will not get better geometry with a coil over set up and rack and pinion. This is likely a simple installation problem that can be easily fixed once it's located.
I seriously doubt this is some kind of inherent geometry issue as my own car runs about half of the parts you have, runs a more aggressive alignment and wheels, and has none of the issues you describe. The scrub radius is not likely the issue, because for this issue to be coming from the scrub radius the force would literally have to be working against the torsion bars to compress the suspension. Even if you have stock torsion bars that would mean ~200 lbs of force to cause a 2" drop. That's not coming from the scrub radius. More than likely there is an issue with the ride height adjustment itself, because that's the only way the 2" drop isn't working against the torsion bar resistance.
If you really want to get rid of something, get rid of the drop spindles. They're not necessary at all at the ride height your car is sitting at in the pictures above. And even if you wanted to lower the car 2", you can do that with the stock spindles by using larger torsion bar diameters and just lowering with the torsion bar adjusters. It does require a little re-working of the bump stops, but that's really minor. I've lowered my car 1 7/8" with factory spindles and 1.12" torsion bars (so the LCA is in fact parallel to the ground and the difference in height between the LCA pivot and lower ball joint is 0)
Do you even have stock torsion bars installed? Or something else?