The strange thing about the factions is that you can still rank up with a bad reputation, so you never really need to worry about blocking progress by making enemies. The system overall seems a little underdeveloped, especially with the lack of mission variety. (Also, there's only one ship to unlock for each faction, and neither is really that great compared to the standard ships, so you won't be missing much.) Killing wanted ships that are allied with the local system can piss off the local security forces, even if they are friendly to you, and will decrease your rep a tiny bit. Doesn't make sense, just an example of two systems that aren't integrated together well. I believe this only holds in a local instance though, so once you jump the sec ships won't follow you. And also, not every ship is allied with a faction, so it is possible to bounty hunt in a faction-neutral way.
The goal of running rares / trading is to upgrade your FSD as quickly as possible (which is usually one of your top goals for any new ship), thereby decreasing the number of jumps required to get around the loop. Ideally you will be at 15-20+ ly per jump laden, which makes each station about 4-5 jumps away, but anything will work starting out. Transit time isn't really that bad, since you hit each system along the way and immediately jump out, but the monotony of the process makes it dull. Also, you'll probably want a fuel scoop to start with, so you don't have to detour and refuel midway through your trip. Each station is <100ly apart, which means your nav computer will be able to plot the entire route in one go (but you have to sit there for a bit and let it think). The loop I'm running right now is just an extended version of the small one that you would upgrade to once you have 50+ cargo space. I use the time to listen to podcasts to keep my sanity.
I started running rares in a stock Sidewinder plus fuel scoop, and the first few trips were painful. However, you soon earn massive profits and can quickly upgrade to a better ship.
This site is also very useful for finding things, if you feel like registering for it (it's free). You can search for locations of ships and upgrades--the prices are standardized across the galaxy, but buying and selling at a particular station will earn rep at that station, which is why some people develop a "home base" and do most of their shopping there--, and it also has tools to find trade routes and rare trading goods. For example, you could use it to make a rare loop only in Alliance space, so you can gain rep faster (as you'll be selling high-valued goods, the rep gains are not insignificant).
The Cobra sounds like a good ship for you; it is nice to be able to do everything in one ship. Just keep in mind that insurance/fuel/repair costs go up significantly with each tier of ship, so it's usually best to wait to upgrade until you have about 1.5 times the price of the ship in credits. This gives you a nice comfortable buffer to work with, should you do something foolish. (Getting a new ship and then "trading" it in for a new Sidewinder is never fun.) If you decide to sell your old ship in the process, be sure to sell/downgrade each module beforehand, since you'll get slightly better value out of the ship--and you can sometimes buy-back upgrades for the new ship at a cheaper price.
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