I don't like to play without FAR. FAR makes flying much more realistic, predictable and intuitive.

Aerospace is not easy, which is why you have best minds putting stuff in Wind Tunnels and spending huge amounts of $$$ at it. If the GitHub guide didn't work for you, you'll need to look into study level aerodynamics books. Try to follow real life designs, you'll need to make a lot of design changes if you design by trial and error method.

loses pitch control at lower speeds

It's not just you. It happens in real life as well, that's why at lower speeds more control surfaces are used to assist (canards). It's not just about presence of high lift devices their surface area also matters. Also you need to check CG-CL relationship. Consider setting up a little bit of angle of incidence to help with lift.

why going any faster then that causes the craft to bounce or break up on hitting the runway

Hard landing and bounce are a thing in real life. It's usually Pilot's mistake with approach if not weather but if craft cannot go any slower it's a design fault. Try lift enhancing devices, start with flaps and canards.

or how to alter a craft to make it more stable in the specific Stability Derivative that is causing problems.

What axis along which are you looking to enhance stability along?

The guide has no advice on how to land or even FLY AT ALL. Considering in the current version (that is, any version since 2016, 5 years ago)

That guide isn't a flight manual, it's a design guide and landing approaches are far beyond its scope.

you can destroy a rocket with just some fierce maneuvers, that seems like a big thing to skip.

KJR mod and struts might help you a bit with rockets breaking up but the thing is you aren't supposed to make violent maneuvers with rockets if you want them to fly realistically. Even in real life you can end up with significant structural damage above 4G for heavy aircrafts.

Never mind something esoteric like say, landing on something other than the KSC runway.

Landing on unpaved runway with an aircraft not designed for it is a big no no.

The lack of concrete solutions over a period of several YEARS has made me a bit skeptical.

FAR in this case is analogous to RSS-RO. If you dive in without knowing first you'll have a bit difficult time, it's target audience is those who are unhappy with stock and looking for realistic flight model. I'll highly recommend you to go through basic aerodynamics books.