The first thing u need to do before almost anything else is to upgrade engines and pilot. I tell you, everytime i play i am not killed before sector 4 or 5. The great achievement of this mod is to reach the boss and of course beat the game.
The prices are so high because is intended, weapons and drones are more powerful than vanilla ones, so they need to be really expensive. Besides, this translates in high prices when u sell any omicron stuff, for example (that is an advantaje as well). Also, you will not be able, for example to use at a time 3 or 4 powerful weapons, like you do in the vanilla game, because thats intented as well, in conjunction with the high prices of every system and everything so you need to think how to configure your ship. In the vanilla game you can have a ship with even teleport, and cloack installed as well and usable and u will have power even to use 4 powerful weapons. This will not be possible in this mod most of the times, so you need to think wat configuration you want for your ship. As for this reason, when you select a class you need to be aware of all the systems available and all the features the ship have, because it will be not so easy to upgrade all the systems and adquire the weapons you want or the defense systems you want, not like in the vanilla game that there is no much sense since the prices are ridiculous sometimes, and u dont need to worry about not having scrap (i always ended with so many scrap in the vanilla game... and with all the systems maximized etc..). If u have a defense mark 2 available, the first thing in conjunction with engines is to upgrade the drone bay. Omicron ships depends a lot on defense systems, so when you have the chance, u need to adquire better defense systems (mark 3, mark 4, ultimate defense). This is difficult, but its really important to pass through later sectors. Engines is the most important thing, cuz this mod is not like vanilla ships, Omicron ships will need to run away a lot of times from a battle. Omicron ships are weak, they have low hp points, so when you see that u almost lose more than half of your hp bar, u need to run away from a battle (because its better to run away, repair and improve something else and return to the battle, to risk more hp points trying to finish an enemy). Because you dont need to worry about the fleet pursuing you, you ca nalways run away and improve some systems or investigate further the other beacons and then return again to the battle.
You just need to try with other classes, the easier ones. Ships that have great firepower like battleships, destroyers, planet killers can survive pretty well if you use the right weapon every time, the important thing is to aim always to the weapon systems of the enemy if you can. If the enemy has a drone bay and it is using attak drones to attack you, aim to the drone bay instead. Its more dangerous to having a drone around your ship than worrying about enemy fire (unless the enemy has missiles and you dont have even a defense mark I). If you have the chance to buy mantis crew, do it. Since when you fight the Omicron renegade ships (in the event) in some cases they will board you and if you manage to kill some of their crew (something that is hard without mantis crew, rock crew are great but is always faster attack, like mantis) you can run away and return again, Omicron ships crew are engi, so they will not be able to repair so fast the systems you destroy (usually using Omicron ships you will be damaging systems instead of just doing hull brute damage and thats one of the tactics to use with omicron ships).
Its hard, but its not impossible , in fact sometimes its easier than it seems, some games are just impossible to advance because FTL is based 50% on luck, and u can encounter a really hard ship just in the first beacon of the first sector (happenede to me xD) and its not the same playing with a vanilla ship with full shield cover than with an Omicron ship.. but thats the point of the mod. If someone is able to beat the boss, i will invite him to a couple of beers
But I was wondering, how did you change the shields so that they only protect certain systems?