Look, do like this first (I've done this):
Just swap the places of the strings where it's possible. Put the "thinnes sounding" string in the place of the thick E-string. Since a nut carved out for a thicker string may very well take a thinner gauge string temporarily for these purposes. Check if the thin sounding FOLLOWS the string. It's no use putting the D at the A slot since the D is thin also.
You can put the thinnest G - string in the A or D string nut slot temporarily. And check if it behaves the same. Now do not put a thicker string in any thinner string gauges nut slot, or you may ruin the nut slot, and it may very well crack as well as the string height will be way off. Now the following:
1. If the weakness follows the string (ie the D is weak too in the thick E-string slot) it may very well be the string sets composition. Regardless of the same gauge, they don't tell us if the inner core is of the same gauge all the way through and just wrapped with thicker wrap. It's called core to wrap ratio. Some manufactureres favors THINNER core even as you go up in gauges for added bending flexibility, however - contrary to popular belief - it is weaker magnetism too. I sure want thicker core as I go down in note, and want's thicker core strings as well as thicker gauge. The "oomph" and "beef" and initial "punch" through the pickups are heard better, if that's the case. Not all magnetism comes from the core of the string, but most of it. Otherwise, just wrap a steel core around a nylon string, put it over any pickup and see what happens.
2. Well then, then it's the pickups. It depends on where the magnets are placed, in the bottom of pickups or the poles have been magnetized or demagnetize. You can get pickus remagnetized, but it's very very hard to get exactly right, and some magnetize them after winding, and some magnetize before winding. If pole pieces arent adjustable something might have happened to them. Pickups (regardless of ceramic, alnico or whatever) can get de-gaussed when just thrown together in pairs, and keep them as handy, while you pick them up from the drawer, if they have been removed from the bass and stuck together laying around in a drawer for a couple of weeks or months. People (not even music stores) knows this. People think they preserve their magnetism by sticking - say - three singlecoild strat pickups together and let their own magnetism hold them together, so that you can pick them up - all three - at once as one package so to speak. This is a no no.
I always had problems with the outer strings, since the magnet fields are sort of running out out there. If it's weak in the middle of the strings, chances are that something has happened to the pole pieces magnetism (individually) or that the radius of the string/neck doesn't follow the staggered pole pieces at all.
If they're not staggered and completely flat, there's the culprit, should the strings/neck have any radius. If the pole pieces are flat and strings are radiused to follow the neck in a "slight arc" the distance from the pole pieces to the A and D string are longer, than the E and G string and thus, poorer/weaker output.
This can't be cured with any pickup height adjustments, or new strings.
EDIT: A properly staggered for radius pole piece on any Ric shoud look like this:
The middle pole pieces are higher. If it has rails (toaster) pickups it should have a slight raidus too, and not flat:
Joey's Bass Notes - Recognizing Rickenbacker Bass Copies
):
