Excellent, All Grain! Excellent!
You're very correct that most of the measurements are on the front end. This is the only place where a brewer can have critical control points to effect the beer. Both quality and repeatability depend on this control. No beer can be any better than the weakest point in the process. I think it's cool that you're going down this path.
White Labs offers lab services to commercial breweries. I attached the PDF. Many of the microbial standards are something you can duplicate in a home brewery. I know there are instructions about making specific growth media out there.
Pre batch, we measure TDS and pH of our source water, as well as our heated water. We compare that reading to our spreadsheet (Bru'n Water) and make any last minute adjustments with Phosphoric acid to balance the RA.
Pre fermentation, we measure gravity, pH, dissolved O2 and temperature. During fermentation, we measure gravity and pH. Occasionally, we are able to do some microbial plating at various points in the process. Post fermentation, we measure gravity, pH and O2. These are all direct measurements.
Calculated measurements are alcohol, calories and real attenuation. At packaging we measure gravity, pH and O2.
The rest is sensory. Through various points in the process, we're evaluating diacetyl, esters, bitterness, color, turbidity, carbonation and sulfur. Once the beer is packaged, myself and most other breweries have a "torture shelf" where beer is subject to heat and other poor storage conditions to accelerate aging. Mostly, I'm looking for diacetyl and oxidation artifacts in these, but I'm also testing for any off flavors or signs of contamination.
I hope that gives you a guide towards the kinds of measurements that'll be useful for you. Except for dissolved O2, I think they're all pretty easy to accomplish.