Sorry to hear about the troubles, but glad you got it working. Congrats! If any of the rest of the original caps act up in the future, well you've already got the replacements. If I could make a suggestion: put the rest all in one container (or ziplock bag, or whatever) and make a clear label of what they're for. At this point you might think there's no way you'd forget. But, trust me, your future self will thank you.
Regarding clumsiness, I'm sure part of that was nerves at doing it for the first time, and also just getting used to the equipment. Though there is one major factor that may have played a key role in the steadiness of your hands that I am kicking myself for not mentioning before now. Do you drink coffee, tea, or any anything with caffeine in it? Caffeine can majorly effect the steadiness of your hands, and it's something most people never realize until they try and do something really precise like this. If you're a regular coffee drinker like me, try skipping it on any day you want to do some soldering. You'd be amazed how much easier it is. Just gotta watch out for the inevitable headache from the lack of your daily dose.
As for accidentally scratching some of the solder mask off a bit of the ground plane, that's not really something to worry about. So long as you didn't actually cut through a trace, it shouldn't be an issue. Especially if we're talking about a ground plane. There's lots of that - and if you somehow severed part of that's necessary, you could solder a wire to reconnect it. Anyway, the only real danger I can think of to scratching the solder mask off is that the bare copper could possibly rust if exposed to enough moisture. But, yeah, if you're worried about it, you did the right thing by covering it.
Oh, and one other thing from an earlier post. Regarding flux, you don't really need a lot. If you've got a flux pen and it puts enough there for you to see, it's probably enough. Like I mentioned earlier in the thread, I prefer to use No-Clean because it's not so dirty (it is fully liquid). But there certain cases where an actual paste makes more sense. Just gotta do more cleanup after. Also, most solder these days has at least some amount of flux built into it. So technically you could get away without using flux at all. Even so, I usually end up using some anyhow. Just makes everything easier. Especially with really old solder on an old PCB that's been sitting for decades (and extra-especially with old solder that is gunked up with dead-capacitor-juice).