...I don't think the mods are gonna like this
Regardless, when this is inevitably moved to GUC, can you actually say what you want help with? (other than the stalking enemies; you posted so much irrelevant data and was so vague I'm guessing you want advice on, essentially, everything, but we can't/don't give aimless advice)
Stalking enemies are either plot-related (as in you're being chased by a guy(s) for a reason), so that's a self-contained number, or, like Fallout 3, there's an indefinite number that just show up from time-to-time so really its up to you...