pancakeman... To be honest, I dont use Lightroom (or aperture for that matter) so I cant speak for their sharpening/raw processing methods. i have used adobe raw in photoshop 4,5 and 5.5 which should be the same method? It has always given me great results. DPP is kinda cumbersome but it does save the different levels of all the camera settings in there so if you have it on a setting of 3 for instance, and you want it at 6, or visa versa, you can always go back in and change it without degrading your image.
This question has been brought up several times on this forum over the least few years... This is such a delicate issue that I dont want to overwhelm you or give you wrong information, however as you know, with the 7D, it is going to point out every single issue with your lenses on a pixel level. That being said, you appear to have some great lenses to put on them so i would first try some rough testing... Try at different lengths and micro adjust ALL your lenses (and test at shallow dof at telephoto...) make sure the focus is spot on.
If you have done that, make sure you are shooting at appropriate shutter speeds... Since this sensor is sooo demanding of the lenses, try shooting a few shots of 2-3-4x the focal length of the lens... if not anything else but to rule out camera shake. If that doesn't solve things, double check what you are focusing on... Since this is going to be sooo demanding on the lens, just the slightest bit off (and sometimes viewing in the viewfinder you may not be able to see if it's a hair off) Try single point or spot single point AF 1 shot AF... see if you cant nail focus. My 7d gives me erratic results at zone AF so I usually just shoot the + (single point with 4 surrounding points) or the single or spot single... those are my best performers. The + shines for me on al servo and motion photography. If still no prevail and if the camera is under warranty, send it in to be checked... make sure it is to factory specs... If this doesn't help, let me know.