It’s the command, they say, that’s the last thing to come when rebounding from Tommy John surgery. And command has kept its latest case, righthander Mike Pelfrey, from assuming a commanding role in the Twins rotation a year after the surgery. The fastball seems fine. It was clocked at 94 miles per hour a couple times on Wednesday — with a little break at the end. It comes down to if Pelfrey is putting his pitches where he wants them. Another problem: the Twins offense, which might need its own reconstructive surgery. The team entered Wednesday having scored no more than four runs in seven straight games. They finally broke through, sort of, in a 4-3 comeback victory over the Philadelphia Phillies. With the Twins trailing 3-2 in the eighth inning, Oswaldo Arcia doubled leading off against Antonio Bastardo. Clete Thomas followed with his fourth hit, a double to score Arcia. Eduardo Escobar bunted to sacrifice and ended up with a hit, and with runners at the corners and Chris Parmelee hitting, Philadelphia righthander Justin De Fratus threw a wild pitch to score Thomas. The Pelfrey Project entered its 13th start of the season on Wednesday — and offered the righthander some reasons to be optimistic. The Twins were encouraged by Pelfrey’s previous outing, during which he pitched into the seventh inning while holding Kansas City to three earned runs. If he could back that up on Wednesday he would have a little momentum. “If we can just build off of that one and keep going from there,” Twins manager Ron Gardenhire said. “His arm strength is better and better and his secondary pitches are coming along better. That tells you he’s starting to have a better feel for things. Now it’s just keep stepping forward.” The bad: He gave up two runs in the first inning when he should have given up at least one fewer. With one out, Ben Revere grounded to third. Jamey Carroll’s throw was toward the first baseline. Justin Morneau caught the throw just as Revere’s left shoulder bumped the glove.