Two steps forward, one step back.
I'm having finish adhesion problems on the body and the new pickup cover. And I used the same process on the neck and original pickup cover and those worked fine. This leads me to believe I've somehow contaminated something in the process.
The pickup cover is minwax jacobean stain around the edges on the walnut (to get closer to the fretboard colour), then a thin layer of system three epoxy sanded lightly with 320, then two coats of minwax wipe on poly. I used this on the original cover and it's dry and smooth. The new cover is still sticky after two days.
The body and neck are two coats of system three epoxy sanded with 320 and two coats of Saman water based polyurethane. The neck is dry and hard as a rock (well, as rock hard as this stuff gets, which is not bad all things considered). The body had sticky patches after 24 hours. The last time I applied Saman, the entire instrument had two coats sanded back and buffed out within 24 hours.
I've now sanded back the body and reapplied it twice.
After the first time, there was a different area that became sticky and didn't fully dry, so off it all came. After that second failure, I decided to sand off the neck even though it seemed okay. I reapplied that one when I did the second attempt on the body and the neck again seemed fine, even though I had that different sticky patch on the body. This time, I decided to leave the neck and only sand back the body. Tonight I did a second reapplication of the finish and so far it looks alright, but we'll see what it's like after work tomorrow.