Tried some of this when transferring to keg (will age it a wee bit to round off some slight rough edges); comments would be:
1. Suspicions regarding caramelisation were correct. Flavours produced are not deep enough to match against the Traquair Jacobite. Next time, caramelise a larger portion of the first runnings (2G, methinks) and do so for a longer period of time (covered to avoid as rapid an evaporation). I'm going to do a little reading on this front before I dive in again.
2. Smokiness works really well in balance with the rest of the flavours: light caramel, light esters from the 1728, plus a moderate amount of alcoholic warmth (not magic marker territory, just... warm, like whisky).
Not perfect, and not particularly close to the inspiration, but still tasty.
FG was 1.020. I'm tempted to up the mashing temp a bit and shoot for 1.030, with increased base grain to reach 1.090 OG.