Riding on a freeway for the first time is daunting, but I think you’ll find that it’s not that scary once you actually do it. I would suggest that you just go as far as one or two exits to begin with and then ride the scenic route home. Next week, go a little further; maybe both ways. Statistically, freeways are actually safer than regular roads I believe.
It sounds like you’re taking this learning process seriously and that’s a good thing.
You have to walk before you can jog and jog before you can run. It’ll be a few years before you become proficient. Oh yes, you’ll be able to control the bike reasonably well long before that, but right now, you don’t know what you don’t know and after a few years, you won’t even be completely sure what you’ve learned that is making you a better rider, but you’ll know you are a better rider by the fact that you begin to have a lot less of those those “ohmigosh I’m gonna die moments”.
Get yourself a copy of “Proficient Motorcycling” by David Hough and that will go a long way to help put an old head on young shoulders. I’ll warn you though, it’s kinda scary in parts and you’ll be riding a lot more cautiously for a while after reading it.
Re. the stop sign, it depends how quickly you slow for the stop sign.
If you’re slowing down slowly, you can slow the bike using the brakes, changing down gears in the normal way as you go (see note below). Alternatively, if you need to slow quickly, it’s okay to brake/pull in the clutch lever and click, click, click your way down to first gear without releasing the clutch until you stop, at which point you either keep the clutch held in or put the bike in neutral and let the clutch out (probably the former for a stop sign). Or, you can use a combination of the two techniqes; the second technique being used towards the end of the slowing down.
No, it’s not a problem to put the bike into first when it’s stopped because you lost the place, but it’s good practice to be in first gear when you stop so that you’re ready to go again. You may find sometimes, that the bike doesn’t want to change gears when it’s stopped if you stopped with the bike in a different gear (or a false neutral). In such cases, if you gently let out the clutch to the beginning of the friction zone while applying pressure to the gear shifter, it will usually help it to shift out of or into the next gear (be very gentle with the clutch though!).
Note: The point of changing down gears (in the normal way) as you slow is (a) so that you don’t stall the engine as the bike slows down, and (b) so that you can be in the correct gear to accelerate away if circumstances suddenly change (e.g. the traffic light changes from red to green while you’re slowing).