With CIS still in effect, then Thor should win the majority. Without it, Wally can win some via massive speedblitz, but Thor can take a beating and if he can get even one attack (especially energy or wind that sends Wally flying against a wall) to connect, he can follow up with just one strike, and The Flash becomes the Fzzzzt.
With CIS: Thor 7-8/10 ('cus Wally will screw something up)
Without CIS: Thor 6/10 (with Wally's wins being accomplished in seconds, and Thor's being absolute splatter-kills)
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While I can go with that train of thought, this creates some intellectual dissonance with much of what is posted on this forum: By that logic, both Superman and Wonder Woman should be able to speedblitz Thor for easy wins (while neither of them are quite as fast as Wally, they make up for it by being uberstrong) -- and I don't agree with that, conceptually, on several levels, as Thor has demonstrated that he can make for viable attacks/defenses against really fast attackers, and can endure massive punishment. Wally will connect with hundreds and thousands of blows (and powerful ones, at that) with Thor, but all Goldielocks has to do is make one of his sweeping attacks connect (which isn't saying it will automatically work, by any means) and the Flash will be off-kilter for at least a second or two; at that point, all Thor needs to do is strike him physically (if in range) or connect with one of his lightning attacks, and the battle is over. Is this a given? No. Not at all. Wally can win a number of battles against Thor. But conceptually, Thor should be able to make the wins agains him, especially if CIS is still on, 'cus Wally, as a character, is much more likely to make an error judgement in terms of combat than Thor is, in terms of executing a series of attacks.
For the sake of the arguement, I'll amend my CIS-off verdict down one grade, to a 5/10 split. But with CIS? Thor. No question. (Now, don't get me wrong: Thor will be hurting like a b!tch for it, at least for the battles where Wally gets some good attacks it...)
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Just to jump in on that: Lightning would be a better follow-up, or dazzle, attack than an initial sweep; while Wally is pounding on Thor, Thor wills a whirlwind of force to eminate from him -- once Wally is moved/slammed against a wall, what-have-you, Thor can follow through with an attack. For all of Wally's ability (which is very considerable, don't get me wrong), he doesn't possess massive endurance or durability -- he can be stunned quite easily by attacks that connect with him, in terms of the power level he's up against. It would only take one solid blow from Thor (via any of his many attack options) to connect with Wally for him to be out of the fight. Thor can withstand a lot of what Wally will be dishing out, and while many of Thor's attacks will fail, the post massive sweep attack will make the follow-up not that tricky.
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More the fact that Thor caused a huge flood can which he done and start frying the water. Heavy winds that would slow flash down or throw him around etc.
I know it's non-canon but Thor is capable to create an Hurricane that covers the entire Planet. He has pretty awesome AE abilities. Wally would have to run for his life, though running is what he is best at. I dunno but Thor seems more then capable to build an AE defense against Wally.
Maybe a stalemate is more appropriate.
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Without CIS and PIS, Flash can easily out blitz Superman or any other High herald. Since blitzing is his only tactic, he can just blitz Thor. Thor is strong enough to kill Wally, maybe even see him coming, but he isn't fast enough to react, or hit Wally despite the 2-3 feats that he has accumulated over 40 years