If I may, I'd like to offer my less detailed, less intellectual view on Clemens vs. Walter and for that matter, comparisons of pitchers from totally different eras. I haven't read everything above in detail yet, and right now I'm at work, so I can't consider everything that has been said so far.
I've expressed my view on cross-era comparisons in other threads, specifically with Babe Ruth and players, and I think that same thought process applies with my view on pitchers and Clemens vs. Walter. When comparing pitchers from totally different eras, I like to imagine the two players in question, Clemens and Walter, were born in the other's era. For instance, imagine Clemens was born in 1887 and Walter was born in 1962. Each grew up learning the other's game - Clemens would've grown up learning the deadball style of game, Walter would've grown up learning a game fully adjusted to the liveball. Clemens would have less need to learn a wider variety of pitches, while Walter would be forced to learn more and develop more pitches besides a fastball in his arsenal.
When considering what I've said above, we must then examine how each pitcher performed in their respective era. I don't have all stats available to me right now, but I know it is very close, and Clemens is still going strong well into his 40's. Johnson's numbers were no doubt ruined by the liveball, and if he had more time to adjust, he would've been better, though probably not as dominant as he was with the deadball. How would Clemens have pitched with the deadball? How would Johnson have pitched with a full career with the liveball? We really don't know, but we can imagine, and I think using this way of comparing cross-era players is fair to both parties.
I do also consider that it is harder to dominate in today's game due to the much bigger and deeper league. The other great pitchers in today's game and during Clemens' career were Martinez, R Johnson, and Maddux, and currently there are many other up-and-coming stars. However, Walter's league certainly wasn't lacking in great pitchers - Mathewson, Alexander, Young, Brown, Walsh, Joss, etc. I'd have to say Walter was clearly the best out of this pack. Is Roger clearly the best out of the other big 3 of his era - Pedro, RJ and Maddux? Dunno.
Just some food for thought.
Red, it took me 16 years to get here. Play me, and you'll get the best I got.