So contrary to my last post, I went out again and it was pretty much agony instantly. Did like half a run and sat down for a good 10 minutes to wait for the balls of my feet to stop throbbing.
The only difference is I haven't been out in a few weeks, and I took the ibuprofen *right* before going up, so it probably wasn't doing anything yet. The rest of the day was mostly fine...a bit of soreness, but I could ride through it.
That tells me that it's either the ibuprofen, or my feet need breaking in if I don't ride often enough...or a bit of both. It doesn't seem like the footbeds are doing anything.
I'll probably stick to what I have for now, and maybe eventually go back to the podiatrist and pay him $400 or whatever for real orthotics that probably will not do anything either.