When we move into actual play, how are you planning to run access to star league equipment? For example, if I have FF armor and need to repair damage, I will need to have it in my supplies. But how does it look to actually buy the FF in the first place? Is it good rep plus connections and bureaucracy or scrounge or just straight up purchase?
Also for custom vehicle (4), what are the limits of customization?
Custom Vehicle 4 has no effect. Custom vehicle is a 2-point trait that is on or off, getting it multiple times has no effect. However, as it is not a "scalable" trait (like Wealth or Vehicle), excess instances of Custom Vehicle cannot be sold back.
Once play begins Equipment becomes available as it becomes available in the game universe. If you're in FWL space in 3049 and FWL doesn't get access to large pulse lasers until 3054 (I don't know - it's an example), then you aren't going to be able to get large pulse lasers there. In that sense, it's actually the simplest possible availability system. No special rules; it's available when its available where you are. Which means that if you're cute and select something like a SNPPC with Well-equipped, you better hope it doesn't get critted out until the early 3060s.
If an item is simply not available, then no level of having Scrounge/etc will help. Once you're in a place/time where it's available, those things all help make it easier to get. IIRC, the base availability modifier for advanced-tech equipment is like a 6, with roughly a +4 modifier within 5 years of its debut, then a +2 modifier for another 5 years, then no more modifier after that. Scrounge and "Bureacracy/faction where you are" and Good Rep (area where you are) and all that stuff can provide positive modifiers to offset that.
I'm just clarifying that I have the correct procedure for how well equipped, custom vee, and mech selection work. With well equipped 2, I get one piece of sldf gear, masc in this case. I choose to roll on the chart, and get my mech. Here is my question, because I rolled on the chart when customizing my mech can I install the MASC in my mech?
No. Gear from Well-connected begins in your warehouse. Once play begins you may install it as per normal StratOps customization rules. DropShips *do* count as maintenance facilities, btw.
I can't seem to find the quirks to know what they do. Where did the you get the charts in your packet from?
They are from the Beta version of the Combat Manual (released ~last month), which also includes the effects of said Quirks. IIRC the PDF is $10 from Catalyst if you care to read the whole thing.