How did the pump become "toast".
I had a TH400 (newly rebuilt by me) that all of a sudden quit propelling my vehicle. Ran maybe 1000 miles before it stopped working.
After I completely tore it back down, I realized that the drive tangs in the pump were halfway ground off, and the drive slots in the converter hub had rounded enges. The *only* way that new seal and the drive tangs/hub could be worn down were because the converter wasn't seated deep enough.
Talked to a friend that owns a tranny shop, he said since almost all converters are rebuilt, when they are machined, they can be machined too "thin", which means the pump and drive don't seat far enough. During re-install (I was broke) I re-used that converter, but added washers under the bolts to the flex plate. After a few miles, the front seal started leaking, which made me pull the converter again, replace the seal, and remove one of the washers between the converter and flexplate, to keep the converter hub weld from hitting that seal. Problem solved after that.
I know on the TH2004R's (at least) they had a problem with the front seal being pushed out. One of the fluid return passages in the pump was designed too small from GM, and builds pressure behind the seal, which eventually forces it out. I would find out if there is a similar problem with certain 700R4's and/or the pumps.
If either the pump or converter were "bad" from the get-go in your case, I'd expect the shop to pay for it, but 13,000 miles is probably outside most places warranty. However, if they installed a shoddy product, I'd still talk with them. 13,000 miles is a pretty long time for it to run then fail though. If something internal were out of alignment, *I'd* expect a seal (at least) to fail long before that, if not bushings, etc.