1. I didn't even know you were allowed 4 (I thought it was limited to 2), but yes, I'm pretty sure you can intercept multiple UFOs
2. I've never had more than 2 in battle (I don't think, can't remember now), so I don't really know the original behaviour, I would expect crafts to follow until able to intercept. Set it up as a Ruleset option as Max Interceptions or something
3. Yes, it should go in the first "available" slot, numerically ordered. Take this example:
# You send 5 craft to attack a UFO
# You minimise 1, 2, and 3 until the 4th arrives, the 5th just follows without engaging
# Craft 2 takes heavy damage, so you minimise return that to base
# You'll want Craft 5 to enter "Slot 2", so you can continue with a 4 craft assault