First of all, the Express is a pretty good van but knowing the way things work underneath, the work that was done seems realistic. It’s interesting that they found it necessary to put in a heavier duty torque converter and upgraded the tranny cooling system on your 3500 since it is the enclosed equivalent of a Silverado three-quarter-ton pickup. Normally, when a salesman specs a truck at the dealership, one of the things that is asked is what kind of service the truck will be used for. It should really be asked when a van is purchased, as well because vans can be used in the same type of tough service as pickups and since the basic construction is the same (other than the surrounding shell) is would make sense to spec the van and pickup alike.
In this case, if I were to have put the spec sheet together on the van, I would have spec’d it for a tranny cooler and heavier duty torque converter, as do most of the truck salesmen I have known. The reason is simple. If the 3500 van and 3500 pickup are doing similar work, they should have similar equipment so if a pickup is going to be doing heavy duty hauling and toting (not necessarily pulling a trailer, but heavy work), then it should be fitted with the transmission cooler heavier duty equipment.
In your van’s case, it obviously wasn’t so the shop did the work that should have been done with the van was ordered. That said, though, it really should have cured the problem. I would tell you to sit down with them and have them explain the repairs they have done thoroughly. If they had rebuilt the tranny to spec then they should also have replaced the clutches, bands, control solenoids and control module as a matter of course. Ask why it was not done as it should have been, if they were doing a total rebuild of your transmission which your question seems to indicate was done. If they answer isn’t satisfactory, contact the owner of the business and ask the same question and if the answer still isn’t satisfactory, contact your local consumer protection office to see what steps you can take.
I would think that since they indicated they did a major rebuild of the transmission that it should be working correctly. Indeed, they should have swapped out the TCM for new on the rebuild without thinking about it. If they tried to used the old TCM with the new rebuilt parts, then they should fix the issue as quickly as possible and then should refund you a portion of the fee you paid because they did not do the work they signed up to do or that should have been done.