If the transmission had been working fine for months on end UNTIL the tuner was used, then obviously the tuner has damaged something. Either the transmission was weak and ready to go anyways or the tuner did indeed damage something. Get it checked at the shop.
As for the catalytic converters, if you changed all 4 and they are retail OEM parts then $1200 does not sound that bad to me. Most people on this forum would only run cheap aftermarket converters that would fail after a year anyways so that is why you'll get alot of responses like that.
BBK H pipe with cats are cheap aftermarket? But anyway the tuner shouldnt have damaged anything. Just revert it back to stock and see if it still does it.