I have e-mailed the support address with a link to a video of some of this.
In the video, you may notice I get a 9 instead of a ( in one case. That is a completely separate layer, but still a shift-modified key.
While recording the video, I believe I figured out what is causing some of my issues, and I'm afraid it could have to do with the silent red switches I selected when ordering. I chose these for the lower operating force, but I believe they also have less travel before activation. For this reason, I suspect I am hitting a new key prior to release of the previous one being detected (for instance, in the example above, I believe I was intermittently hitting D before fully releasing Enter, so the release of Enter was triggering the release of Shift even though D is shift modified). One instance not shown in the video that is different, but may have the same root cause is that I often get $# when trying to type $3, but $4 always works fine. In this case, a shift modified 4 is under my index finger with a 3 under my middle finger, but the not-shift-modified 4 requires use of the same index finger. I suspect that the 3 is triggering before the shift-modified 4 release is detected, and that obviously can't happen with the 4.
I think this helps me understand the key modifier conundrum better, but it seems solvable. For instance:
Regarding my shift-modified layer, if the layer key was holding shift, no other key would need to be modified (so it would also work for mouse clicks). That would only solve half of the problem, though, because I also want to be able to shift-lock, so I'm not sure how I'd pull that off unless layer modification was an option so shift would always be held while in the layer or a macro could be triggered to hold shift until another macro was triggered to release it (that would be less ideal than layer modification, but either one could be a rabbit hole).
Regarding the $# vs $3 issue (which is only an example and certainly happens with other key combinations such as %3, #4, and +4), it might be possible to very briefly delay sending the keystroke for a non-modified key when it occurs after a modified key. This could be similar to a debounce in practice, or it could include some logic to see if the prior key is being released or not.
In case it is helpful when deciphering some of the key sequences discussed, I am also attaching my current layout to this post. FWIW, the "RMod" note on it refers to a key that doesn't exist due to the layer limit in place at the time when I created the layout (IOW, now I remember what the additional layer I wanted was for).