Alrighty, here's the update:
Met up with 240kid at my local shop today and went over the car. I couldn't seem to recreate it just sitting there, and the shop mech couldn't do it while driving (shoulda told him to switch, I can make it happen anytime except while sitting around, it seems). Anyway, the shop mech says it's probably the Injen CAI making the whistle, apparently Civics are more notorious for whistling intakes, but it's common on a lot of cars. So, Michael and I took off the filter (car off, of course) and went over it, looks to be in pretty good condition, I'll probably clean in in the next little while just for good measure. The mech said it's pretty much a sign of a well-working intake, and said the filter looked great too, so no worries on the whistle.
Next, the heat on the shifter. I took off the interior panel and got up under the dust boot to the... well.. dunno the name, I'll call it boot #3. Boot #3 was a little off to the side, so it appears air was indeed leaking up through that boot and causing the heat. I adjusted the boot carefully, I don't think there'll be any more leaks, and the heat did seem to go down a bit (hot day though, I'll feel it next time I'm out at night).
Thus, I'm pretty sure the car is just fine, and my paranoia sense is satisfied, so it's all good. It was great to meet up with a fellow NICOnaut though, so it wasn't a wasted day

. Thanks 204kid.