1. What's the fastest way to train them and how does their ranking system work? Is it just about the rank enemies have you kill while they're deployed, or do they have to make the kill or hit the target to count for their progression?
Ranking system works much the same way as it does for CMDRs, NPCs just rank up about ten times as fast.
Fastest way to rank them is to give them control of a strong mothership in a combat area with a large number of high rank targets (CZs, Haz RES, Compromised Nav beacons, etc) while you pilot the fighter yourself.
2. Which SLF would you recommend using? Including the guardian SLFs (unlocked all three).
Depends on precisely what you are doing and who is going to be flying them.
None of the guardian SLFs are particularly good, outside a few specialized tasks.
NPCs in general are bad with the Taipan.
Gimbaled laser fighters are decent for ranking very low rank NPCs, but are mostly useless for higher rank ones or for any CMDR that can aim.
The fixed beam GU-97 is probably the best all-round anti-SLF fighter. It's a bit soft and a bit slow, but it's the most agile (both in rotationals and vertical/lateral acceleration) and packs as much of a punch as any fixed beam SLF with heatsinks.
The fixed beam Taipan is probably the most potent SLF in the hands of a CMDR. It's mobility is good enough for a real pilot that knows what they are doing and it's much more durable than the GU-97. However, NPC crew struggles with the mediocre rotationals and if you send an NPC in a Taipan against an NPC in a GU-97, the GU-97 will win most of the time, even with a moderate rank disadvantage.
The Fixed MC Condor is a good pursuit craft (fast, longest range and low WEP draw weapons) and is solid against most NPC hulls.
Keep in mind that there is still a bug with SLFs where they will eventually cause lag/rubberbanding problems for other CMDRs in the instance.