The module "misalignment" matters not one bit. What you call a module is more commonly called a magnetic pick up. All it is is a little tiny magnetic field generator. When any reluctor tooth enters that field, the field strength changes. The ECU senses the change in the field strength and fires the coil. That's all there is to it. So parallelism plays no part in it, nor does the reluctor gap much.The reluctor gap just needs to be big enough so that it doesn't actually touch the pick-up when the Vcan starts tugging the base plate around, and small enough to ensure a strong signal is generated for the ECU. That is why the large spec. I have found by experimentation that the Orange-ECU will read the signal with any gap from zero to about .030, generated by the factory original pick-ups.So I set mine to about .013 and call it done.
Now, let's talk about the surge.
There are only three things that can cause a surge that varies with throttle;1) is the vcan hunting, which is super rare, and 2) is an unstable powervalve or dancing metering rods, and 3) is a lean low-speed circuit
So, plumb your vacuum gauge to manifold vacuum with a long enough hose to bring it into the cabin, or jam it under a wiperblade where you can read it while cruising, the take it for a ride and observe the gauge during the surging. Then head back to the shop. Now,start the engine, and loosen the metering rod piston covers. Rotate them a quarter turn and snug them down. Can you see the pistons? You need to see them. Next run the rpm up in park until the vacuum decreases to that noted during surging, and watch the pistons. If they start dancing,there is your problem; you will need different,lighter springs.They need to stay down.
If the rpm goes over 3600rpm abandon the test. Instead pull the PCV hose off the valve and introduce a vacuum leak there large enough to drop the gauge into the surge zone previously noted.
Ok so let's assume the pistons are firmly locked down. Shut off the engine and put everything back together. If the pistons were not dancing,then neither would the Vcan be.
So that just leaves a lean low-speed circuit.
This circuit is comprised mainly by the transfer slot, and any/all air leaking into the engine through or around the butterflies, and also thru the idle air bleeds. It is augumented by the idle discharge system. The carb was designed that with a correct wet-fuel-level, and when these two are in the correct working relationship, then there will be no surging.
This correct relationship is known as the T-port sync.So click on the little blue M below, and get your T-port sync set up; then a take her out for a new roadtest.
Now let's talk about your surge,lol. The above is for a steady-state surge. Your surge is no surge at all. Pull a couple of plugs out. My guess is they will be carbon fouled from running very rich. If not, then the ignition system is crapp. Or the pick-up polarity is reversed.
So what say the plugs?