I am not sure how screws in runners will help align the fence. I've seen a few of your jigs where you use similar techniques, which all make sense.
In this case, it is the squareness of the fence.
I have the runners on and fairly good fit, a bit of binding, however that is down to my saw more than anything else. I then raise the blade through it, and the kerf "should" never change, as the blade to runners to base is fixed.
Then i attached the fence as square as i could manage by using square against the slot i'd just cut, cut 4 times round a board, found i was out by 12 thou, added a shim of 3 thou, rescrewed one end of fence, was out by 4, same again, and was sorted, 2 thou over about 4 feet.
the really odd thing is that i then wanted to make a 45 deg mitre attachment, and started with a square, which i cut in half to get "close enough" to 45%, figuring i would use one angle for half the mitres, and the other for the other half, so if i had 45.5 and 44.5, they would still fit perfectly and be undetectable to the eye.
It did not work, so i check the 90 deg angle, as that is the only one that has to be right, right? and we all know that the corners of a triangle add up to 180 deg.
well, i have invented new trigonometry, as according to my red gem 0.1deg digital angle measuring thingy, calibrated at 0 deg on a planer bed, and 90 deg with a good square, and double checked numerous times... i have angles of 90, 45.4 and 45....