The car looks great, and I'm loving that you're planning to wrench on it yourself! The E46 platform is so ubiquitous that there are basically DIY guides for everything, and there's at least one member on here that is active that has done one of those maintenance items, so you're in good hands.

Re: learning a manual transmission - I learned on manual transmissions when I got my learner's permit so I can't help you from that perspective. As a painful refrain like everyone else around here: it takes time. You said you've only taking it out for a spin about a dozen occasions and that really isn't that much experience.

Some tips that might help you:
Learn where the clutch engages. Go to a parking lot that's flat or has a very small uphill grade and just use the clutch to hold the car or get the car going without using the gas pedal. Repeat this multiple times, decreasing the time from when you let off the brake to when you hold/get the car moving, to get a feel for the clutch engagement point.
Sit in the car for five minutes and row the gears. Get familiar with the position of each gear. Do this a couple of times until it's more muscle memory.

The other stuff will just come with experience. Knowing the clutch engagement point, what gear your in, where to move the shift lever, etc all becomes second nature with enough seat time. Shifting smoothly is a life-long pursuit. The 1-2 shift is still the hardest for me and I'll flub it from time to time. I think it's down to the difference in revs vs. wheel speed so the margin of error is smaller compared to other gear shifts (I'm probably talking nonsense, but it's what I tell myself).

Also, driving a stick in stop-start traffic is work. It's not fun. If that's what I found myself driving in 95% of the time, I'd get sick of it too. But I specifically search out less crowded roads if I have to drive during rush hour, even if it'll add 10-15 mins of the commute.

As for the long shifter throws and long clutch pedal - yeah, you can change them. I left my clutch pedal alone aside from a CDV delete, but I got a short shifter from UUC. Short shifters are a must, IMO, but some people would argue otherwise. Your shifter could probably benefit from new shims at the very least, they've got some serious wear at your mileage which would clean up a lot of slop if present.