1. SHIII (ocassionally SHIV)
2. Yes, most definitely. Going through the manual and working out examples from practice missions helped tremendously.
3. Depends really. For long range convoy interception I'll use mobo to work out an intercept course, but for lone targets I happen to stumble across it's usually much easier to work out the speed and AOB on the fly by using Hitman's whizwheel.
TMA, on the other hand, is something I've been practicing a lot. I'm able to work out reasonably close estimates of the target's course (a course I already know from the mission builder) but speed is proving to be a bit more difficult. I can workout a few estimates based on slow/med/fast speeds but I still need to invest more time in doing the advanced stuff that you hinted on in the manual.
4. Yes. I use Mobo in place of
this method when doing TMA.