Already stated above, I've come to a lot of problems regarding the level design and how to deal with certain events going on during the game. I also figured out that putting the maps of level 1 and 2 together is probably the best option. Entity placements is crucial in the game, because to have to find out what happened by yourself. and you can not trust anyone else.
Level 1 was about you waking up in the areas and then you find a way up. When arriving somewhere you got yourself inside a military FOB while facing the gore and abomination that have taken over the facility. many aspects of level 1 are plain. Find the airlock override, Get to the office complex and then get yourself to the military controlled areas.
It was a hard choice for me to make. But I decided to throw both levels in the trashcan and start from scratch. All because they were not perfect.
I will keep you guys posted on any changes. and I will try to put some pictures on the Image page ASAP.