The injuries to Beckett, shortstop Julio Lugo and center fielder Coco Crisp would typically be classified as typical nags of Spring Training. But with the altered schedule, Francona is doing his best to try to gauge who will be available for the start of the season.
"We have a lot of moving parts right now on this trip," said Francona. "The normal Spring Training aches and pains today don't seem so normal because we leave in a week. We need to remind ourselves of that, we need to make good decisions, also being aware that we're leaving. We'll be ready, we've just got to get everything sorted out."
Lugo, sidelined with lower back tightness, is confident he will be at shortstop when the bell rings in Tokyo.
"I'll be ready," Lugo said.
For Beckett, it seems as if it will be the opposite.
The right-hander came out of Saturday's game following one warmup toss because of back spasms and has been up and down in the ensuing days.
On Tuesday, things were better.
"Better today than I was yesterday, that's for sure," said Beckett. "I got a good night's sleep."
In Francona's session with the Boston media earlier on Tuesday, he didn't completely rule out Beckett pitching on Opening Day.
"I don't know that we would want to eliminate it today because we don't have to," Francona said. "The one thing we're not going to do is send him over there to pitch three innings and hurt his back. Just like everything, it depends on how they're doing health-wise. He had a good day today. As the day progressed, he looked like he was moving around a little bit, which was good."
"We just want him to be healthy for the long haul," added Francona. "Last year, when he had that [right-finger] avulsion, we didn't run him out there when we probably could have, because we didn't think it made sense. In something like this, we'll do the same thing. We'll use good judgment. It's not always easy to use good judgment, but it's the right thing to do."
With Daisuke Matsuzaka's wife expected to give birth at some point next week, the Red Sox might play their first two games without their top two starting pitchers.
Jon Lester and Tim Wakefield are the pitchers who would likely be called on if Beckett and Matsuzaka both miss their starts. Wakefield said after his start on Tuesday that he hasn't been told that he'll be stepping in for Beckett or Matsuzaka. As far as he knows, he's pitching the second exhibition game in Tokyo.
But Wakefield also said that making the adjustment and starting one of the first two regular-season games instead wouldn't be a big deal.
"With that scenario, I'd just be pushed back an extra day or so," said Wakefield.
Crisp is battling back from soreness in his groin. The timing couldn't be worse for the center fielder, who is battling Jacoby Ellsbury for the starting spot.
While Lugo eased his way back into baseball activities on Tuesday, Crisp was still confined to indoor workouts.
Despite Lugo's optimism about being ready for Opening Day, Francona will make sure to look at the big picture.
"We're trying to kind of stay on him a little bit because I think he's trying to go maybe too quick, and he set himself back last time," Francona said. "We'll see where he is at the end of the week."
Despite all the uncertainty, Francona is determined not to turn the trip into a crutch for his team.
"We're going to go play wherever they tell us to play, whenever they tell us to play," Francona said. "If we screw it up, that's our own fault. So I'd rather not do that."