A couple of thoughts...

To check how much you have to lower the dovetail bit, pull the two
boards apart as hard as you can, and use feeler gauges to measure the
biggest gap. Lower the bit that much(*). I use a 1.5hp (yea, right)
PC router with the fixed base, and I've calculated how many thou each
tic on the ring represents so I can do this "accurately" (again, yeah
right).

Beware of cupped boards.

I always do two corners at a time, one on each end of the jig. Not
only is it faster, but it keeps the jig squarer to the boards. At
least put a spacer on the other end, using one of your other milled
boards.

Yes, your router base should be flat. Compare it to some reference
flat, not to the jig. I got a cheap granite surface plate from
Grizzly for this purpose.

Don't rotate the router when routing - hold it in a fixed orientation
throughout. Consistency is more important than concentricity.

When I do through dovetails for batch jobs, I do all the tail boards
first, then all the pin boards, and it doesn't matter which tail
boards I match up with which pin boards - all the joints are the same.
The D4 *can* make accurate joints, so keep working on it.


(*) If that's way too tight, next time do half the thickness, I lose
track of when the adjustment doubles the results and when it
doesn't.