Did the engine get jacked up or moved around or mounts worked on at all? If the engine (or trans) moved it can tweak the shift linkage relation to the transmission. I'm not sure it's possible to be "between" gears in the shift selector, but I'd double check the shift linkage if it were me...
May also be worth bypassing that trans cooler for a few minutes just to rule it out (or a kink in the line?). New stuff, if it goes bad, tends to go bad quickly.. So it's good to rule out other new parts that have anything to do with the trans.