Well the first part there for the cable. Do your self a favor and spend the extra amount for a honda cable. If cheaped out and got a motion pro cable and the push cable(one on top) seemed to shrink. No matter how I routed it, it would not go on right. SO right now, I am running just the pull cable. As for cleaning things up, I am not sure what you would clean up. The cables are pretty large and so trying to thread them through the bars might not work. You might be able to get aftermarket controls to clean things up some but that would be additional cost but might be ok if you are doing a cafe or bobber.
The tube in the third pic, I have no idea!
It goes to the back of the bike and is probably some sort of vent. Keep it clear and forget about it.
The item under the carbs that you are pointing to is the housing for the cam chain tension unit.
You will probably want to pull it off and as long as you do not mutilate the gasket, you can reuse it.
Loosen the bolts but be careful, it is under spring pressure in there. Clean it up, old oil builds up in there and gums things up.
Oh, and welcome to the forum!
The ride IS the adventure. The destination is just to get gas!