I don't remember you mentioning mods in your previous post. I have found a few problems running mods myself, and there is always a potential problem running several mods in tandem as they may clash.
IMHO, you don't need to run mods when playing the single player game. I know myslef that it seems hard the first time you play it but the more you play FL the easier you find it.
One thing that might be the problem - when you are playing the missions try to always keep the contact list - bottom left corner - set to ! show important items. This will always show mission objectives and enemy ships. If you set it to "Ships" then you won't see trade lane rings and shield generators.
Another possible reason is that when you drop out of formation near the arch you are 3 or 4 km away (approx) and there are a lot of ships in the way so the shield generators are going to be at the bottom of your contact list - as it is sorted by nearest object. You may even have to get close to the arch before Ozu tells you to go for the generators and they show up in the contact list.
My best advice is to restart and ditch the mods. If you do, my tip for the starting system, NY, is to hang around in the bars at Battleship Missouri and Fort Bush, you never know what useful info you might pick up there
- you may need to pay a couple of visits tho'. I'm on my 4th time playing the plot and have never seen any bugs with it.
My other tip is to try to buy a Defender as soon as you have done the first mission. You will be told how may credits you are short. You should be pleasantly surprised that you don't need that many to get a ship upgrade and don't forget the tip above as well.
regards..