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So, Mechanically I have this thing tuned up nicely. I spent some time making sure all the towers were perpendicular to the bed etc. I ran through the advanced calibration procedure several times. It all worked out great. I think mechanically/electically this thing is about as good as it is going to get.

Now I want to start troubleshooting some minor printing issues and fine tuning the rest of things. My last printer had me start tuning the extruder as the next step after getting it mechanically setup correctly.

On my other printer it came with info on setting the E steps and tuning the filament etc. I had to measure the filament and enter the exact dimensions. Print some specific objects, take measurements, adjust the E steps. etc. I had some directions to follow. I actually got nice prints without much issues doing this. No boogers, no stringing, dimensionally accurate, etc. I got a little Z banding and some issues with tall ABS prints splitting, but I can tell what is causing that. I am upgrading my other printer now with prints off the Rostock V3 to correct these.

I can find some guides and tips here to help, but it seems kind of random and not really a simple step by step guide. It is really too much info to make much use of it starting out. They do link to a guide written by someone on here, but it is not step by step but rather a cluster of tips and tricks with some philosophy and stories thrown in. It mostly just says to try this and try that and record it and make small changes etc. It does not necessarily tell you how to initially dial things in or where to move things based on what the print is doing. Its more common advice if your in engineering and electronic of making small single changes and recording everything. I know it is great info, but is there a step by step process to dial it in? I have not seen any mention of adjusting E steps in the documentation. I am not sure where to go next but I am hoping for something a little more precise or basic with step A, step B, step C etc (if it exists). I am using MatterControl for this printer and I use Slic3R and pronterface for the other, so its a bit different.

A calibration cube comes out with dimensions that are very good.
The issue is that I am getting boogers on PLA and ABS.
I am getting stringing on PLA also.
Bridges could be better on both
Otherwise I am making usable prints. They just require more clean up work than they should.

I am not finding a step by step tuning process for the Rostock V3. Maybe there isn't one and you never adjust E-steps? I don't know.....
Looking for some advice.

I also wonder if I should switch to another software that can do all my printers well so I can get good at one software and tune all the printers essentially the same. S3D was suggested to me by a local guy where I was buying filament, but I didnt get into specifics. He did say he had 55 printers. That is another topic I suppose, but it could relate to tuning my printers more efficiently.

Your extruder steps per mm calibration should adjust to a specific linear length of filament, and that should remain relatively constant. What you'll need to adjust in your slicer for every filament is the filament diameter itself.

Recommendation for the "steps per mm calibration"?

Does this mean your expected to pull the PTFE tube out of the hot end and perform the method of extruding 100mm and measuring and then adjusting the value? This is the best way? Taking that tube out is a little bit of a pain. I did it once and then made a clog because I didn't get it all the way back in. Since then I have printed that little tool. I also didn't know at the time that tightening that nut grabbed the tube. I thought the push lock did all the work. I guess you could pull the tube from the extruder side and do it from there (if this method is even what you mean)?

Yes, that basically is it.
If you want to do it precisely, you could try to use this: https://www.thingiverse.com/thing:2598993
Still have to try it myself though.

I leave the extruder steps/mm and the slicer extrusion factor alone. When I start a new roll of filament, I do a test print and adjust the extrusion factor on-the-fly until I find a setting that gives neither under nor over extrusion. Then I use that setting for the rest of that roll. It's normally between 95% and 105%.

Incidentally, the steps/mm for standard hobbed shaft extruder drives can increase by as much as 15% at high extrusion speeds compared to low speed extrusion. This has been confirmed by measurements taken by several different 3D printer users. We've just introduced nonlinear extrusion compensation in RepRapFirmware to allow you to compensate for it.