is the only one who can't really be confirmed,
I'd be out of character for him, as he never once was good, that is why we should call it confirmed he's the exception amongst the R3 robots. The guy's even of alien origin to establish him as different even more. Besides, as of Battle and Chase, the guy created a ninja temple filled with traps! Doubt the government would like that. NapalmMan on the other hand decided to be peaceful and create a museum. I'd say it's possible for some of these Wily made's to do something beneficial for society, but only out of their own desires, nothing forced. That's just the quirkiness of the series.
Now, I'm confused with why everyone's referencing Rockman Rockman. Isn't it just a reboot of the original?
Rockman Rockman is Rockman, just as much as Irregular Hunter X is RockmanX. It's just the first games with the details that were always in the books included into the plot (either as established in the first game, or in subsequent titles), there's some new additions, yes. But the intend of both games always was to have the same story told in a modern manner. To give a prime example, interview has confirmed that the Day of Sigma was originally supposed to be scenes we already knew, that happened before X1, then they decided to make it grander as fanservice. Writers of the Day of Sigma were thus given the explicit order to keep stick to the original plot of RockmanX as close as possible.
Given everything, there's obvious attempts to keep the series as a single continuity. As such these remakes shouldn't be able to affect what we see in titles that are not going to be remade. Such things as discarding games would only make a mess.
IHX after all references the likes of X8 and RZOCW, to the point that it was advertised as telling us "Sigma's true reason for rebelling!" going with the irregular at will train of thought promoted in X8. There's also the case that newer games follow both the remake and the originals, as with Rockman9's release.
All in all, some details might change, such as Penguin's height, but it's still one series and both the remake and the original have validity to the whole that is the Rockman series. It's not like in Castlevania where games are outright discarded because they wrote themselves into a corner. And it's note like Zelda where the grand plan of the canon is a complete unknown. Rockman in general is THE most coherent plotwise of the classic series. Only Metroid rivals it. Where Rockman has issues with the grand amount of games released and Capcom's inability to close plotlines, Metroid has far less games but has to deal with the Prime series tying into the old games in the end.
The creation of the Guts-Dozer remains a mystery and can never be proved, but we can safely say it was made from the original Guts Man. I think Guts Man's parts (hench the extra copies), and possibly brain were used in his making.
I really don't think we can safely assume it's the original when it can't be proven... As Gauntlet said, why would the original be deactivated and put into a museum? It'd be reducing a character to a mere display figure.