Well I'll give my opinions on some of these.
1.) SR wasn't designed for minis use like later D&D editions. Minis work fine with it, but there is no standard "threat range" for being in melee. Basically if no one has starting trying to melee the other one, I wouldn't consider them to be in melee (as it would appear they are both trying to stay out of melee). I would say anyone that has attacked in melee on their last action or been attacked by melee on someones last action and not moved would probably be in melee.
That said, the Interception rule (SR4A pg. 161) states that if a character moves within one meter of an enemy and tries to continue movement without attacking, the enemy gets to spend a free action for a free melee attack. So when enemies get close to each other, it makes it unlikely for them to stay out of melee for long. Once one tries to run away, or move, they are going to get thwapped most likely.
2.) You have to be moving stealthily for infiltration, but there aren't really cover limits by RAW. Rather than limitations, anyone viewing gets bonuses or you get penalties depending on the circumstances. Chameleon suits definitely help keep your stealthiness, but they aren't full invis., so remember they help you remain unseen, they don't prevent you from being seen.
Attacking someone (assuming in melee) is probably going to give them a bonus to know which direction the attack came from, but they'd still have to detect you to find you. Of course, they probably have enough to go on for making a blind attack against you at that point. Everyone around is going to have to find you to attack you, but depending on circumstances they might have enough to go on for blind attacks, or they might just spray the area and blame Joe (the guy you attacked)'s swiss cheese nature on you if they drop you. Varies from enemy to enemy really. It isn't D&D, attacking doesn't cause the chameleon suit spell to break. That said, any action like that is going to spark a new perception test to spot you (most likely with a higher DP since they'll get +3 for actively searching rather than -2 for being distracted).
3.) Depends largely on the force and nature of the spirit. Stupid (low force and/or watcher) spirits probably will go word for word at your instructions simply because they cannot think to understand more. (Don't tell a watcher to search every corner of a building or it will tell you what it found in every corner of the building but it won't look anywhere else in the building). Smarter spirits should be able to do some basic reasoning on their own. There is a distinct difference between protect me and protect me and my buddies, but if hostiles start throwing lead around you and it looks like you're on their to do list, a decent force spirit should be able to reason this is a situation where protect me should apply.
All that said, how you treat your spirits can directly influence how they treat you. Treat them like suicide bombers and slaves, they may hold you directly to your wording despite "knowing better". Treat them well and they might try harder to please you, going out of their way to be of more use.
4.) It largely depends on what you mean by goes down. If you mean unconscious then I think the spirit would stick around and follow it's service (especially if ti's bound). If you mean dead, well then the spirit is free to do whatever it wants, which probably depends on how the mage treated it and how big of a douche the person that axed him is. Someone may be along to correct me later (magic isn't my strong point), so take this with a grain of salt.