how is your saddle tilted? If it's tilted forward, even slightly, you might find yourself shifting forward. That would be the first thing I'd check. I'd start with it dead level (using a level!) and then maybe even adjust it a tiny bit nose up.

As for the other rules of thumb you mentioned:

The KOPS (Knee Over Pedal Spindle) / plumb bob method you used is really only good to get an objective measurement of saddle fore/aft position. It isn't necessarily the correct position. Other than having a professional fitting, the way I've figured this out is just by "feel of balance" over the pedals. I happen to like mine about 1/2 - 1 cm rear of KOPS.

Sometimes the fact that you feel you have to shift yourself back can be related to the level, but also it might be your body telling you that it wants to be a little rearward of your current position.

Or it might be telling you the stem is too long.

The front axle is obscured" method of determining stem lenth: Again, this isn't necessarily the ideal position for you, and doesn't account for stem height (rise or drop w/a a flipped up or flipped down stem). I don't know what to say here except that I personally experimented with 2 or 3 stem lengths, flipped up and down, and just decided what one I liked best. This was after I settled on liking the saddle position mentioned above.

I'd do the saddle level and after you've tried that for a couple of rides (maybe tweaking as you see fit), then try shifting it backwards a little to see if that makes a difference. Then, I'd mess with the stem length and rise.

It's all inter related, and unless you actually have a pro fitter look at you, all you can do is think about these principles and experiment.

Not much help I know, but there ya go...