After driving her around for a few days, getting the other issues cleared up before she's inspected, I think the noise is fairly minor. I still want to address it, though.
Keep in mind, the Baja is my primary vehicle, but I drive a company car for work. They let me drive it home, so the Baja won't see much in the way of miles.
I'll wait 'til next month when we've got a bit more cash flow coming in, then pull the engine. If the input shaft on the tranny looks good, I'll swap the clutch components for new. I may as well, if I'm looking right at them. Once I know, I'll report back here.