Okay, after analyzing my options to death, here is what I come up with. To be clear, I will pull and install the trans, but I don't have the expertise to crack it open for repair. I also want that 4.3 final drive while it's open.
Option #1: Buy a used 60k mile transmission for $1200ish (including shipping), pay for the LSD swap and install of the 4.3 final drive. All said and done, I'd have about $2500 into it. This unit might last forever or might not, as condition will be somewhat "unknown."
Option #2: Clarke. Their unit would be $3200 + shipping + $2400 core + return of core +optional $1k WDC treatment. I assume the 4.3 install would cost extra labor, even during regular assembly (plus parts). In theory, I could sell my Wavetrac LSD ($600ish). While this might be the "best" option, there are questions about how much better for a track exclusive car. The polishing and deburring undoubtedly reduces heat and friction, but the longevity benefits are not measurable. The WDC treatment appears to be the same, promising less friction and heat, and with some vague references to increasing strength. The inclusion of the carbon fiber syncros is nice, but also not necessarily something that has measurable longevity improvements on track. Lastly, it appears they repurpose used internals, albeit after careful inspection and the polishing; I get it's debatable on whether that matters. But, almost certainly the enormous $2400 core charge would indicate they need 100% working internals to be reused . . . and I almost certainly won't get all of that back since my transmission went boom. All in all, I'm sure going this way would result in the "best" transmission, but I'd probably be into it for at least $5500 plus whatever part of my core they don't return. How much better is where I'm sure opinions abound.
Option #3: I can get a brand new transmission from Ford for $2400 and no shipping (local dealer). The core is only $600, and almost certainly NOT dependent on my trans being in working order, so I would expect it back. The 4.3 parts will be $600 (I have an OEM turbo credit coming from Whoosh), and my local speed shop will do the LSD swap and 4.3 upgrade for $600. All in all, I'd be into this option for about $3600. Would be a new transmission with new internals, albeit not polished and/or treated.
Option #4: Let someone crack open mine and only fix what's broken. Obviously, total cost to do this depends on the extent of the broken parts, and there may or may not be a backorder on whatever broke. What's not broken is reused. Note, my car has 113k miles on it. My guess is that I'd be into this option for $2500-$3000 by the time I buy parts, pay for labor, get the 4.3, etc. And, most of the parts would be 10 years old and have 113k miles on them.
I think Option #3 is the winner.
@kevinatfms