This weekend was a productive one; I swapped axles in the wife's truck and then dealt with my computer to retrieve that sweep file.
I ran it initially at 50% like you suggested and then up to about 80% "throttle" on the Yamaha, no ill effects and very similar results like I experienced with AudioTool. I like that a bit more for leak checking and to check pop. Although for fear of burning out my woofer's voice coils I didn't run either of those hard enough to produce pop. I'll run it some more today but didn't notice the PR's moving all that much. So I pulled the 128Hs again and swapped cabinets. I also checked each by moving them in and out by hand. The woofer which makes the popping noise rubs at the last 1/4" of outward travel. The other woofer is just fine by comparison. So I suspect either the pole piece is out of alignment or the recone job on it was trash. It's better than it used to be, but the rub is still there.
Marantz stuff still out of commission. That must be F'd up pretty good.
If someone can link a video which shows how the PR300's should be moving in relation to the 128Hs' action, that would be incredibly useful to me.