Thanks all for your help.
Spent some more time tonight, and I think I've got it sorted. Here's where I ended up - in case anyone's interested.
The bog off idle was solved with setting the needle jet one notch richer [clip @ 5th position from top]. I tried leaning it out one notch first, but that made it considerably worse. I'm now maxed out for richness without going to a different needle. I may look into that after my ride this weekend - I know it's not ideal to be on the richest setting. This seems to have solved the hot running too - which makes sense. This created a bit of a flat spot at the transition from the needle circuit to the main jet. Richening the air mix screw and adjusting idle position accordingly seemed to help with that. May try out a bigger main jet in the future.
To recap, in case anyone has the same setup and is looking for a starting point - here's my current setup. Running well so far - and HUGE 'get up and go' improvement over stock.
1999 KTM 640 LC4 Enduro
KTM 'Supermoto' slip-on [see photo below]
Stock headers and 'S' section
Airbox snorkel removed and opening slightly enlarged [I'm guessing... by the ragged edge on the hole. This was done by PO]
Drilled carb slide holes for faster throttle response [.125"]
150 main jet
Stock needle @ richest setting [clip at 5th position from top]
47.5 pilot jet
Mix screw ~2.75 turns out