He should be well and truly over his injury by now with 4 or 5 matches under his belt this season, including a decent effort in AO qualifying.
I agree about the "runs" of good and bad form within a match - in fact most players suffer from this to an extent - the skill I guess is to minimise this and have enough weapons/know-how to battle through at least your service games when you are stuggling momentarily. Who can forget James at Wimbledon, where for one set in R1 vs Andujar he was, frankly, unplayable. James won it 6-0, and even that didn't do justice to how well he was striking the ball. So he certainly has an A game up there with the top 100, but his B game lets him down.
For me his biggest challenge is his second serve, which match facts would suggest is simply not good enough at this level. Whether its a speed, placement or (lack of) variety problem, I don't know. Very often the success %age gap between 1st and 2nd serves is huge for James - which means if he is going through a "bad" patch in the match with low first serve percentages and more UEs, he drops his serve more often than not. His return game is average, which means he can't rely on it to get him out of trouble on serve (as Andy often does, although far less than he used to, as both his first AND second serves have improved).
Either way, James will be disappointed to lose matches like this, even when playing below his best. And a tournament final or even win was a real possibility, given the weak draw. Strange.