Check brushes in the alternator, but I doubt this is the problem
I would first look for voltage drop problems either or both in hot harness or in ground leg I'm not intimately familiar with these computers so I don't know where the reference ground is, so you need to refer to the diagram and find out. Essentially, there are several things that all need to be "at the same level." By this I mean within hundred's of one volt
the engine block
the body frame
the negative side of the regulator (computer ground whatever that is)
the battery negative post
On the "hot" side of things the same thing is true. There are several things that when operating need to be within a few hundredth's of one volt of one another
the battery positive post
whatever the hot supply to the computer is
the voltage sensing to the regulator if it's different from above
Because I'm not familiar with your wiring, I'm going to revert back to a typical factory Mopar harness, and ask you to visualize in your mind the "voltage path" that is involved with "let's say" a 69 Dart ----This is just an example as means of explanation........
The hot path to the regulator, which is the voltage sense, is:
From battery.....starter relay.....fuse link......through bulkhead connector.....to ammeter....through ammeter....back out ammeter......past welded harness splice......ignition switch connector.....through switch......out switch connector.....back out bulkhead connector.......to switched loads under hood (and voltage regulator)
The ground...........
From battery NEG.........to block........to ground cable........to body ground.......to regulator mount flange
Each and every one of those points mentioned is a place you can have a poor connection.
If there IS voltage drop and or poor connections in either or both the above, you can have this type of surging, and you can also have overcharging, as the voltage regulator "thinks" it is sensing low voltage.
You can also create what are known as a "ground loop" and this can also happen in the hot harness. A ground loop is a general term for a situation where a multiple ground path can cause "bad things" usually this type of "cyclic" activity. This can be caused by such things as a poor connection...........The voltage sags, the poor connection loses conductivity, and the regulator says "crap, CHARGE" and the voltage surges up, the connection "makes" across and the voltage suddenly jumps up, and it repeats, oscillates over and over.
This can also be caused by something causing some sort of TIME CONSTANT. This could be something like a STEREO AMP with a great big filter capacitor charging and discharging. Something in the added on circuitry of your EFI stuff (not familiar) might be doing this
HOW TO FIND
Check documentation for the GROUND for the ECU. Temporarily run a great big ground wire to a known ground point. (By the way, if you have a trunk mount battery with a separate ground cable, this might be a problem)
Google SINGLE POINT GROUNDING. This helps prevent ground loops.
For the "hot" side, find the main ignition / energizer feed for the computer and temporarily run a LARGE (say no 12) jumper / hot wire from there to the battery.