1-How much should I really let the bike warm up before ridding it?
If you are using the recommended 10-40W oil viscosity, none, assuming the oil light is dark, but working properly.
Just don't wail on the throttle until it will accelerate as normal without any choke.
... for now I will let it idle a couple minutes then take it easy for the first few miles before giving it too many rev's.. (adjusting the idle at stop lights as need be.. before it settles down at about 12-1300) It also makes a light kuckluck sound when its idling much lower then that
I never readjust idle while operating. Warm up, idle up, is done with the right hand on the throttle. When it is warm it idles right where it was adjusted last time it was warm.
Warm up concerns are not so much the revs as the load placed on internal parts. Keep the Rs down below 5000 while warming to save the cam lobes and followers.
The warmed engine was made to be revved. See the tach, it says anything below 9200 is wonderful. It is.
The Kluckluck is uneven cylinder firing pulses, changing the rotational speed of the crank, and trans gears. The gears alternate contact engagement of of tooth gear tooth sides. Pulling in the clutch will change to pitch as it change the mass and the force needed to change rotational speed. Some bike can be made quiet with careful carb vacuum balance. Others, do it because of uneven cam wear or other items that make the cylinders fire with slightly different strength at idle.
2-Is it ok to primarily use the kickstart? was it designed mostly as a backup? (the electric start works great, but i really enjoy kicking it over)
Kickstarter has "endless" life, and can be used for full time duty. I drove my 74 for 2 years straight with a weak battery, unable to electric start. Then the battery got REALLY bad.
3-The paint is in flawless condition and unfortunately I will be keeping the bike outside most of the time... how important is it for me to get a cover for it? would a half cover like this http://www.newenough.com/parts/accessories/covers/dowco/guardian_traveler_motorcycle_cover.html be enough? Should I invest in a full cover? preferably I would have something that could still fit under the seat but I dont know how reasonable that is. What about covering most of the metal on the bike with something to protect it.. What should I know keeping the bike outside?
Weathering is going to make the bike look worse corespondent to the severity of exposure. Here in California the sun will damage everything exposed, vinyl, paint, plastic, rubber, etc. Water and ice will also create it's own type of damage. Acid rain = bad.
Best solution is a heated garage, of course. A full cover probably next best. But, some covers with not breath and trap condensation under it. A humid environments like that with accelerate metal corrosion. Not only for looks, but all the electrical connections will corrode/oxidize.
A half cover is good for block sun damage effects, yet allows good ventilation to dry things inside it.
4-The bike really does not like to be under about 3000 and first gear is fairly touchy, this is all normal right?
Pretty much, Though I don't know what you mean by "touchy". Throttle operation should be predictable/reliable in any gear. But, if you are snapping the throttle full open at low RPM, you can expect it to wheeze before any power occurs. Up to 1/2 total throttle travel should give reliable acceleration, with the lower gears allowing the revs to build the fastest.
I am much more used to driving cars and shifting sooner to save gas when I dont need the power, but I understand that will also drain the battery.. so around town I usually keep it at about 3500-4000
Cars don't usually have a 9200 red line. Your RPM selection is normal and the lowest reasonable while in traffic. The stock muffler allows it the still be pretty quiet. Other mufflers will usually draw attention and annoy others, possibly even the driver.
5-Shifting into neutral can sometimes be almost impossible and other times is very easy.. but seems to have little relation to how warm the bike is
This can be a simple clutch adjustment, or inadequate oil integrity, or friction plate warpage. At any rate, it is a clutch issue.
Minor clutch drag can be tolerated by keeping the rear wheel turning while making the selection.
6-The clutch gives quite a bit of resistance to hold (my reason for shifting into neutral when I can at a long stoplight) How easy is it to adjust/change this?
The springs in the clutch increase resistance when compressed in a linear fashion. For this reason, the clutch actuator uses an over-center concept. This creates an non-linear pressure advance as it is actuated. It trades increasing travel distance for less required force applied.
The over-center positioning point is adjusted on the clutch cover. Then the cables are adjusted to position the clutch lever in a comfortable position, while still achieving both full engagement and disengagement of the clutch.
From your descriptions 5 and 6, I would try to readjust the clutch to ensure full disengagement. If you get this right, the force needed to hold the clutch in will be less than what is needed at mid-clutch lever travel.
Cheers,