They are almost different bikes.
I've answered this before somewhere....but here goes.
Tuoldo (Gen 1) 02 - 05
Taller & larger than later model, based on the 2003 mille.
Single headlight etc.
You sit ON it when you ride.
V990 engine with 51mm TB's about 113 RWHP
Single can, 2-1 exhaust - flat spot in power from 5-6k, then loads.
Engine does produce a bit more grunt at low (2-3k) revs.
Tunuo (Gen 2) 06 - 09
Smaller and lower than early version, based on 06 RSVR
twin headlights, tail as per RSVR
You sit IN it to ride, much more like a japanese bike feel. Feet further forward.
Ti or Evo Engines 54 or 57mm TB's dependant on age, about 121 or 126 rwhp.
Twin Exhausts, linear power - but bias towards top end.
Rough model history
02 - Tuono R model. Carbon, Ohlins and Oz parts. Limited edition,rare & georgious
03 - Tuono Fighter. Tulip red/Gold, Magnet grey/Gold. Black Brembo wheels. Showa/Sachs. Plastic bodywork
03 - Tuono Racing. Black, yellow number boards. Carbon bodywork, Ohlins, white Oz wheels. Also race bellypan, nose and other bits. Close ratio gearbox.
04 - Tuono R (again) Black/red wheels, Silver/red wheels, Fluoro red/black wheels, Showa/Sachs. Basically same as Fighter model but new colours
04 - Factory. Similar to Racing, blue Oz wheels, Ohlins. white number boards. No race gear.
05 - None produced - they are 04's
06 - New Model based on RSVR. uses Titanium series engine. Blue Oz looky-likey wheels, Showa/sachs suspension, colours, red/black or black/grey or silver/grey.
07 (07.5 USA) Evo Engine, colours red/black, matte black/grey, or blue/white - so called "Greek flag".
07 - Factory. Evo Engine, Red Lions head tank Oz wheels (blue at first, gold later), Ohlins suspension, Carbon bodywork.
08 - R model new colours - white replaced black/grey
09 - R model colours - silver, blue/white & Orange
09 - Factory - Black dream colour scheme
I might not have all the colours right for the last year or so - as it's difficult to establish exactly when they change, and the importer still had stock of some colours. I haven't covered some of the really tiny details but it should be a rough guide.