CNC cut stringer notches

If the stringer material is to be 3/4 inch, have the notch cut to about 3/8 inch at the location where the stringers will not be 90 degrees to the frame . This will position the stringer on the frame.
When the frames are installed, install a 3/8th inch batten into the slots. The batten will of course be distorted as it is being forced to go through the frame at 90 degrees.
With a small hand saw, relieve the batten by chamfering the slot. Note you need to work on all the narrow slots at the same time. When the 3/8 original slots are relieved and the 3/8 inch batten follows a smooth curve , just increase the width to the 3/4 slot that you require for the 3/4 stringers, opening up each side of the slot the same amount.

Before the new composite materials, in the early 70's, we built maybe a dozen 22 foot
Ultralight kayaks, using 3/8 ply frames and 1/2 by 3/4 inch deep stringers,
Then stapled ceconite over the the structure. Ceconite used for airplane wing, fuselage construction, shrinks when heated with an iron. We then would tighten it up with the iron, dope it and have an extremely light kayak. As we did not have heavy frames or wide stringers to work with, we could not just run screws through the joint
Just glued the extremely snug joint and tapped in a finishing nail to hold the joint while the glue dried