You swapped tires with another Spyder, your tires / wheels did not shake on the other Spyder.
Your Spyder continued to shake with the loaner tires / wheels.
Therefore it is not front tires / wheels at this time.
The rotating parts that can induce a vibration at this point would be the rear wheel / tire. Though that would require a respectable imbalance.
Therefore, an easy test, wipe the area where the rear wheel balance weights reside, mark the wheel. Then remove those rear wheel weights. Was a change experienced. Take notes. If needed, the weights can be prepped and reinstalled at the witness marks.
Any worthy dealer knows there is a TSB regarding belt vibration, and should have, under warranty made adjustments to lower belt tension to the TSB specs. It appears you may attempt this yourself. Try it and note any change.
As for an alignment causing a vibration, very unlikely, and supposedly that was accomplished. Suggest checking accuracy yourself by using tape measures and marking the tire by raising it, spinning and drawing a line upon the tread. Accomplish marking both tires. With a helper, verify the dimension across the front is about no more than 1/4”. Measurement should be at the same heights and as far above the ground as the frame allows. Take good notes of the dimension.
As for the windscreen test, suggest removing it entirely, leave off, test ride without the windscreen. Take notes.
While troubleshooting by eliminating one item at a time can be time consuming, hopefully it offers up a noticed change that leads to a corrective action.
I am helping a friend, his customer has a recently purchased aircraft that has a vibration. Using similar logic, we have eliminated the common items that cause vibrations, tried various other techniques to demonstrate a change, and I myself assisted in dynamic balancing the prop to .025 IPS, which is well below the typical threshold of .1 IPS.
Downside here is now it gets expensive, partially open the engine checking crankshaft dampers, after that it is complete engine teardown / overhaul at a cost more than a fully optioned new Spyder, or we buy a new prop, but hunch says it is internal engine, or dynamic incompatibility of the engine and prop.
Point being, a couple of quality hours spent loving your Spyder might reveal a best course.