To eliminate as many variables as possible, including poor focus calibration, test the lens....
- in good light on a contrasty, flat subject (e.g. a box with crisp print and patterns);
- using a tripod to eliminate shake or focus shift from photographer wobble;
- with Live View and 10X magnification to examine the target/subject closely;
- and Live AF (to get focus bang on).
You don't need to take a shot, simply evaluate the image in Live View. If the image is unacceptably soft then you've got a lens with poor optical IQ. It needs dealing with. If it's sharp then at least you know the glass is good.
The next step is to check AF calibration accuracy. Switch from Live AF to Quick AF and try focusing again. Does the image soften? If so you have an AF calibration problem. You might be able to correct the error with microadjustment, but it is possible that the adjustment required at 400mm may differ from that required at 100mm or in between. Maybe you can find a good working compromise, or if you spend 90% of the time at 400mm then optimise the lens for that focal length and let the rest make do.
If the image remains sharp with Quick AF then the conclusion to draw would be that either the IS is failing you when hand holding or there is some problem with technique.
It's worth a reminder that the high pixel density of the 7D is going to reveal problems with kit or technique with far less mercy than any of its predecessors - if you are viewing at 100% to judge IQ.
FWIW, after spending a few years mucking about with AF microadjustment for many of my lenses, including the 100-400, I finally bit the bullet and took two of my bodies and five lenses into Canon and let them sort it all out. The bodies (7D and 1D3) and a couple of lenses were within warranty. Two other lenses cost £30 each to have calibrated outside warranty. The 100-400 went in for a zoom tension repair as well as calibration and that cost £127 in total. Everything came back dead nuts. That was from Canon at Elstree.
If you ever find yourself anywhere near Upminster, or we bump into each other on a TP meet and you have your 100-400 handy I'd be happy to have a look at it for you.