My friend with a Bullitt has had his redone twice since new for similar problems. The first time there was no TSB and the Dealer just replaced the syncros. The second time they did it was per the Tremec TR3650 TSB and all is ok. He does have an extended warrenty on his so it was no charge to him.
The strength of the 3650 is good, it's just the early ones have shifting problems. As far as replacing what you have, I'd either go with one of the TKO's or a 6-speed and be done with it.
The 500 and 600 are most popular, but they need other parts to adapt to the replacement of the 3650. There are kits out that have all that is needed.
D&D has trans and kits that come complete, here's their link: http://www.ddperformance.com/