Hi Peter,
i have built a number of strip builts and first, you are doing all the right things by setting it up and testing with some strips before you start stapling/glueing a lot of things.
so the first thing i would say, based on your description, is that if this is about the deck it's fundamentally what is going to look right/best and you don't have to worry about any performance, structural or handling issues. the second thing i would say, is it's not uncommon with a long boat, even one that comes from a kit, to have some misalignments develop that you have to address. if you are building from plans, its even more challenging....everything in a kit is computer cut.
so your approach to shimming up the bulkhead and bending the apron up a bit is just fine if visually, you like the look.
on how things can go wrong, a common problem in building from plans is not properly addressing the thickness of the material in any part and the consequence on various sections when they are skinned with a 1/4 inch skin and how that interacts with a real build. plans generally do not have an adjustment for skinning/construction, they are just the sections.
the second thing is key reference marks that can reliably be relied upon and confirmed. in a traditional strip built (not hybrid), you have a strong back and a clear mark on ever section on how it lines up on the strong back and its easy to check with a laser or other effective level or reference line. on a hybrid, you build ontop of a hull....which is not as easy to line up as a strongback.
the third thing is little differences can easily accumulate in a build and with the length can get multiplied in terms of how they may interact.
fourth, you might just have cut something wrong and not recognized it.
and fifth, maybe something actually is a way it is but you did not have that in your minds eye and therefore are judging it as wrong when it is what the designer intended.
anyway....all kinds of fun sources of error....i have seen a lot over the years.
h