some of your answers
if you are invading a border c3, the occupational units are great, i usually use sf for the same reason. one thing you didn't mention, when clearing the air d, you'll need to have a ground unit with in 35km of the target.
as far as the hj for destroying targets go. i like your thinking. but how many attacks will that take? in interest of time, you'd be better off usuing ha/ht, they are rather cheap. and to expand on your statement "the precision bomber will take out ground defenses," that is true, but bombers will not clear the lt/la/j/av. use drones or mrmb
as for clearing gars, i've found the cheapest way is a bomber/drone unit, and then switching to a ground unit with ha/ht to finish it off. the fastest way, is to use mrmb and ha/ht in the same unit, use the mrmb to clear the gar, and with out switching units, you can switch weapons to the ht/ha (switching off the mrmb,)
for air dropping. your way is fine, but theirs a trick to making that work. probably the better way, would be to drop your sf, (i usually use 3,) then you go about things normally, clearing air d, and painting, of course. the difference, you clear gars with *only* bombers, and then use cruise to destroy targets. although, bombers are more efficient destroying factories, use the cruise on cities and forts.
i rarely use navies against c3s, and i haven't sence they made some changes. i'm not upto date on navies, sorry
general questions
cruise missles, land or sea, are probably more effective than guide missles, except for clear helis.
ha/ht over all are the cheapest way to destroy a target, after gars are clear. yes you can go cheaper with hj, and hav, but do you really wanna click 10+ times to destroy each target? depending on the quality of your units, it can take as few as 1200 total of the 2 ht/ha (600 of each for example,)
bombers versus mrmb... well, their are several things to consider. bombs are easier to buy, in a day to day thing. but bombs aren't very good at destroying forts. so when you get to the forts, you can burn through the bombs, or switch weapons. switching weapons (units,) takes time. so using mrmb to clear forts, and bombers for the rest... thats my answer.
as far as looting the c3, you can transfer much of it out via the transfer options under the empire menu. you can set all the gars to "undefended," and get that stuff 2. you can make worker exchanges for the workers you need. however, the non-military stock... only way is to make direct sales to your other countries, and transfer the money back. that last part i find just isn't worth the time.