Yes....you are over thinking things.
throwing out numbers like .03125"......from both sides......with a file........is gonna make you give up before you even start.
Being a machinist can be a huge asset to you while making knives. But being a good knifemaker means knowing when to shut the machinist off. Save the precision measurements for fit and finish.
You're about to start making knives, truly by hand, with files. No easy task but it certainly can be done.
Scribe two lines on your blade edge and spine that leave a strip about .030" wide right in the center. File down to your lines and take your primary bevels up as high as you can. Keep both sides as flat and as even as possible.
The biggest issue I see with files is leaving the blade (mostly the edge) thick enough to survive heat treating without cracking or too much warping, but then being able to thin hardened steel down thin enough to be a good slicer with files.
.060" is way too thick for a primary bevel termination. Even with a secondary bevel, unless it was huge, it will have the cutting geometry of a splitting maul.
If I had to make a knife with files only, I'd shoot for .015"- .020" max on the edge and hope for the best in heat treating.
Even grinds, even heating, good thermal cycling/stress relief, NOT over-heating, avoiding side to side swirling or stirring motions in quenching, and even cooling are the key things to consider when trying to minimize warp. Even then, it still happens.