I think Willkie could have won if FDR hadn't run in 1940, he was a quite popular candidate with a good chance of breaking the New Deal coalition. Even with FDR in the race he came close in the polls.
Willkie was fundamentally an internationalist, and it's likely Pearl Harbour would occur anyway. However if he's elected he might have coattails, which could make it too risky to pass a Lend-Lease program and it could fail. If that happens WWII would be altered, though somebody else can specify exactly how.
IOTL Willkie died in 1944, and as his VP died earlier in the year that would leave his Secretary of State as President. However he died IOTL because he'd been careless about his health and ignored multiple heart attacks and warning signs. So while he'd be under far more stress as President his health would also be cared for more.
I'm not sure about civil rights. The Democrats controlled Congress in this period so they would probably obstruct any civil rights bill. While Willkie could do Truman's military segregation he would not be able to really combat Jim Crow, only until the 1960s could it fall and the civil rights movement was pretty lucky IOTL. Truman and FDR did a lot for civil rights IOTL, so Willkie would probably be similar.
I think he might try to reform the New Deal and make it more pro-business. When Republicans won in 1952 IOTL, they didn't do so, but that's because they'd been out of power for 22 years and FDR's policies were so entrenched. TTL they have only been out of power for 8 years. I think they would be less afraid to tinker with the New Deal a bit and it would be les entrenched. But the fundamental programs, such as Social Security, would survive.
Can we find Willkie's 1940 platform for a better idea?