Do a search for 'Rectifier lineage", it's been a heavily covered topic around here. There's a ton of good info.
In short, yes there ARE differences.
* 4 different circuit board revisions, C, D, F and finally current rev. G
(which includes later 2 channels and all 3 channel models)
* Output Transformer (slight difference)
* serial loop (much nicer) on early 2 channels
* attached power cable
There are slight differences in all the Rec lineage and it is subjective.
As a Mesa player who has had several 2 channel Rec's including a 99 TR, 03 SR, a 97 DR and finally my 93, I can say with complete confidence that there is a big advantage in knowing that the tone on these early
Dual Rectifiers reigns supreme. The newer 3 channels are great, alot of people love their sound, they are still great amps. I use to sell Mesa's when I worked for GC, I've heard and tested them ALL extensively.
My favorite high gain amp is still my early Holy Grail '93 Rev F/serial loop...the best to my ears....hands down, no hype !