I'm sorry; I don't buy the "big giant butterfly net". The problem is that the outcome of the Spanish-American War can't just be divorced from reality. It had a major impact on America's view of itself and its role in the world. Altering the outcome of the war can't just have no effects due to handwavium. It creates logical contradictions that I don't think you can resolve.
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Certainly, no Philippines also means no Guam. If the Americans are not going to grab up the former, they're not going to go to the trouble of annexing the latter, either. These alterations change the American approach to the Pacific. We must keep in mind that even after the attack on Pearl Harbor, FDR went out of his way to stress how American Hawaii was. He had to do that, because public opinion polls had shown that a lrge number of Americans didn't consider any of the Pacific holdings (including Hawaii!) to be "really American".
If Hawaii is America's lonely outpost in the Pacific, this feeling of it being an isolated forward position will be further strengthened. I'd wager that the absence of the Philippines and Guam will entail that after World War I (assuming for the moment this occurs as we know it), the USA will not want to take responsibility for the Northern Mariana Islands and (OTL) American Samoa.
This changes the USA's Pacific strategy yet further (to the tune of 'the barely being a Pacific strategy'). I really doubt that your assumption of the USA still imposing sanctions on Japan for its invasion and occupation of French Indochina in 1941 actually holds up. I'd tend towards the opposite conclusion: that this ATL USA would refrain from such sanctions, and consider it a big load of "not my business".
This would make any war between the USA and Japan pretty improbable.
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What's more, though, I also think that the whole premise of "the USA doesn't annex the Philippines (but does annex the other OTL gains from the Spanish-American War)" is just very implausible. When we look at what the American government actually did, and how it kept its own negotiators in the dark about the plans to actually annex the Philippines, this isn't something you can just wave away.
I believe that for the annexation of the Philippines to be most plausibly avoided, you'd have to keep the imperialist faction out of power (or somehow kick them out of power right after the war.) This would necessitate William Jennings Bryan winning in 1896 (preferably) or 1900 (as a back-up option).
That scenario, to be clear, would hav far more wide-spread ramifications. Even if a war against Spain still gets fought (which isn't improbable at all), there will be no annexations afterwards. No Philippines, no Guam, no Puerto Rico, no foothold in Cuba. No later interest in getting a hold on the Northern Mariana Islands and on (OTL) American Samoa, either.
And if we go with the 1896 POD... no annexation of Hawaii, either. (Which also means no Palmyra Atoll, for whatever that's worth).
Which all adds up to: no war between the USA and Japan. It's not just improbable in this scenario, it's vanishingly unlikely. But beyond that, this ATL scenario completely alters the American perception of itself. In the resulting ATL, the USA will almost certainly refrain from getting involved in any European conflicts.
