1. Dynamic relations.
If You have trouble with this consider doing missions only for Teladi- This way You will end up being enemies with Yaki only.
If You need to get something from race or faction use agents to boost Your relations to desired level (or just to fix it). Easiest way to get them is to do passenger missions (so fast TP class ship is usefull here) which have "+Agent" listed in rewards. If the thing You want is a station You can always use agent to steal blueprint and build it in HQ.
2. Avoid using Universe Traders.
I've given up on those after some testing. It is better to use sector trader which can trade in range of several jumps from home sector (This way You can control which race/faction reputation will decrease/increase in time). In my version of universe I have used 4 Chokaro in Teladi sectors just to supply HQ with money for basic expenses.
3. Do not spend discovery points on things that can be obtained through agents or money. Use it to get unique ship blueprints for HQ (like pirate ship TS as a cheap and fast TS that can be produced in HQ).
Explorers Guild Representative can be found on equipment dock, shipyard, military base, research base etc. Just not on regular station with production cycle.
4. Automated Nividium mining is good source of money.
Take a look at NNMC Shipyard in PTNI Headquarters beta. Good starting setup is to buy one Pelican Miner (TM) which will work as a carrier for 3 Falcon Miners (one Mobile Drilling System per Falcon is ok).
Just make sure all gates are 5jumps away from nearest enemy sectors and it should be peacefull again. Hub is small, easy to defend so later in game consider building Lasertower production complex and install ~200 Lasertowers in it (eject 5 at once in one spot, move away like 1km, drop another 5- I have used this to guard all gates and pester ships that (somehow) manage to get through blockade). It will became deathtrap to Your enemies
6. Access to high demand market where You can sell ANY amount of products.
It works for Nividium too. Later in game You can buy TL to sell all those goodies from large complexes linking XXL sized factories...
8. Cargo Bay Hacker can be used to steal wares from station too. This can be good source of income in early game.
11. Complex planner is excellent design tool. Just remember Build Command software has limitations - final step requires sufficient cargo space in TL to load ALL extension kits at once - if it fails due to insufficient cargo space You can connect stations manually, just remember to place sub hubs 1st and connect them to final hub in one go. Alternatively You can use construction service which seems to not have such limitation. Also make sure everything is balanced in the same station upgrade level (for example XL sized stations)in case if You want to upgrade complex later. Summary shows amounts produced/required per hour.
12. Ultimate cash source.
14. Blastclaw prototype is M3 class ship that can deploy 5 marines to capture target. You can use that to train marines when doing retrieve abandoned ship missions AND M3 class ship can be docked on TM class ship.
15. Consider carefully where You want to install Engine Tunnings which You find during exploration.
In my 1st game-play I have installed most on my M5 exploration ship (Advanced Kestrel) of choice leaving not many for TM and none for TP. Fast M5 exploration ship is nice but more than 700-800 speed is not needed while extra speed on TM and TP is a lot more usefull later in game.
16. Capturing ship in sector full of enemies.
Just fly into it within fast TM ship, go as far away from center as possible until Triplex scanner is clear, then switch ship to fast M5, order TM to fly further away and cirlce enemies in M5 ship (make sure not to be spotted by enemies on the way back). If You are carefull You can draw away enemies from gate or target slower ship giving You enough time required to capture it.
It is very usefull to claim sector if You want to protect it too. If AI claims it before You any kills in it will affect reputation with owning race. if You do not plan to put defenses in it just let AI do it, if not claim it to avoid reputation issues.
Lastly I would like to say Thank You for letting me play X3:FL for free. I really enjoy it despite some minor flaws it has:)