I've never drilled a slide, never felt the need to, so I can't comment on whether it helps or not.
I'm not familiar with that Y-104 needle. How long is it from the top clip slot to the tip? It has the best chance of working if it's close to the 50mm length that the stock ones were.
You said you found your old carb parts. If that carb kit you got is the Heiden Tuning one then, as Skull mentioned, it's not very well suited to a stock sized 650. Apparently Heiden designed it to work with the 750 big bore kit and their own 2-1 exhaust. Most guys with more stock bikes haven't had very good luck with it. The needles in it also differ in length from the stock ones.
We always seem to be coming back to the needles. I don't think you'll get it tuned very well until you get some around the same length as stock. Then on top of that, those pleated pods you have will most likely also cause some tuning issues. Glad I'm not trying to tune that thing, lol.