The 100-400 (1st generation) is known for needing afma (auto-focus micro-adjustment) and for having a lot of sample variation. It might be worth looking into that. On the other hand, if you are used to getting sharp images with that lens on that body, it sounds less likely. Are you indeed using the same camera body as you were? You say that they seem to all be outside the plane of focus, and that does sound like a focus problem. Afma can fix that, if it’s not too far off. Read up on afma before trying it, as it can make things worse, apparently (never did it myself.
Try doing some test shots in a controlled setup to see if it’s *possible* to get the image quality your used to seeing. Tripod, mirror lockup, remote release, immobile test target, live-view focus, etc. (Also test your autofocus while your at it) If you still can’t get what you think it should be giving you, then it might have gotten dis-aligned, damaged, or something and might need a repair. The 100-400 with it’s trombone-style zoom has the reputation of getting a lot of dust sucked into it, so it might be worth a check, although it would take a *lot* of dust to affect image quality. Just shine a flashlight in the camera end and look into it from the opposite end and everything will become apparent.
Good luck with that!