Alright here goes... Let's see if I can remember to cover everything I wanted to.
MAP: Good job on the map. I like the way it says station beacon and turns green instead of red. You might like the open sign, but you might be able to also have a (I don't know what the exact right term is so...) "Bat Signal" type light coming from the station that is either green or red (or nothing) depending on whether the signal is on or off.
How are you planning on using the signal in game? I would think you could use the "No Fuel" text list to spawn most normal events, you could turn on the signal to attract everyone good, bad, traders, pirates, Rebels, Feds. And when you turn it off you have a higher chance of being left alone and maybe you could take the time to make some free repairs to your hull or something, maybe only the Fed will be able to find you when the Beacon is off but occasionally Rebels will stumble across you, I'm not entirely sure.
ENGINES: Having 1 power in Engines is necessary so I am fine with having at least a small evasion chance, I would say either limit engines in every hostile event or leave them on all the time for consistency. I accept your explanation that they might be able to miss you on their own, but being able to increase your evasion by having a pilot and engine man is a bit strange. Also, since you can't actually dodge, very well at least, you are going to take lot's of hits and so you'll need your crew to repair systems, breaches, and put out fires more, which should actually add an interesting dynamic and be very fun. Which brings me to my next item...
REPAIRS AND HULL: Since you will always have access to a store you will always be able to repair after a fight. I thought this would be imbalanced at first, but then I thought about it some more. Since it costs scrap it might not be a good idea because then you will never have enough scrap to upgrade your other systems and you will eventually die. So there will be this constant decision making of should you repair your hull or should you upgrade your systems, sometimes you might not have enough scrap to make repairs. Just like in vanilla FTL you will probably be leaving your hull at &60-75 in hopes of finding an event that will let you make cheap or free repairs.
If you want to increase the maximum hull strength of the station I would say use 60 instead of 35, because 35 is just awkward, or just stick to 30. Here is a mod that created alternate hull strength indicators for other people to download and use, you could use one of them:
http://www.ftlgame.com/forum/viewtopic.php?f=11&t=21578I talked about how turning the Station beacon off might allow you to make some repairs for cheap or free. This could be a good strategy to wait until you have about half hull and then try to make some free repairs.
STORE & UPGRADES: Have you tested the "ship inspector" thing where the store changes whenever a certain event happens? I'm just concerned about this working since it didn't wok when I did it a different way.
From an event standpoint you could also have the event be an event where a trader comes to your ship and "restocks" your supplies, unloads new passengers, etc... Meaning you know have new stuff available. New merchants have set up shop in your station.
I think that using the reactor to track progress is a genius idea. I was wondering if the reactor actually worked like the other systems.
As far as how many "Levels" of enemies you could have some thing like (10 or less)-(10-12)-(12-14)-(14-16)-(16-18)-(18-20)-(20-22)-(22-25), that's 8 levels. Or you could have half as many levels and just have increments of 4 instead.
As far as rewards for enemies go... The only thing that seems to increase each sector is the amount of scrap, not the resources they give. So I would actually say, keep the dynamic rewards, ("LOW" "MEDIUM" "HIGH" "WEAPON" "DRONE" etc...) and just add a bit of scrap for higher level enemies in addition. So level 2 would give 5 extra, 3 would give, 10 extra, that's just an example though.
And by adding events that give you free reactor upgrades you will have the same "push factor" as in normal FTL . It won't be too hard to create different difficulties in this way. You'll just have eight different text lists for each difficulty.
SHIP GRAPHICS AND UI: It looks like the station is working OK the vertical way it is now, but the weapon mount's are a bit wonky. You could rotate the station the same direction as the other player ships. it would actually be pretty cool to see them from that angle.
You could also remove the red warning for no fuel and just replace it with the normal graphic so you don't think you have a problem.
And I'm not sure what exactly is the cause of that weird triangle, but I'm pretty sure that triangle image is located loose (knot in a sub-folder') in the images file. It's called "null resource" or something. You could replace the image with a fully transparent image and that should fix it.
OTHER STUFF: You'll probably be using all of CE's stations so that will give you 7 different stations for each of the different factions. Sleeper just created a new AI station too so maybe you could use that one as well. That is eight. The only thing you'll need is a Crystal station and one other station, maybe you could make a stealth station?
To make all of the stations be able to use all of the different systems though you will need at least 14 rooms on each. (10 main systems (Medbay & Clonebay are the same) + 4 Subsystems). Luckily the federation station already has 14 rooms, unless you want to have an artillery stem and a blank "docking bay". Of course you could do what the Peregrine custom ship did and make the doors room the docking bay.