This archetype is not meant to be balanced next to the vanilla rogue. The goal here was to make a class that was better at skills and combat than a slayer/investigator even multiclass character. I still want the slayer to be "better" at combat and the investigator to still be generally better at skills.
I could use some suggestions and feedback.
I would begin by increasing the size of the text (even if only by one point), decreasing the space between paragraphs, and removing all mention of the class features you have removed. I certainly don't have perfect visions, but your document is a little hard on my eyes.
This is not exactly an archetype, as the flavor you have provided is more or less the same as a CRB rogue. It strikes me more as a rogue re-write.
The language needs to be tidied up. Try to match languge that exists in other Pathfinder material. Obviosuly, there will always be interpretation involved, but it is better to allow for less of it.
Precision Strike
This simply feels like it is too much. I see it as pretty abusable at 1st, and too good for a 1 level dip. The definition of vulnerable is vague. Are creatures in heavy armor susceptible? However, if you kept the ability as is, it could be rewritten as:
A rogue gains a bonus to attack and damage rolls anytime her target suffers a penalty to speed or armor class, or when the rogue flanks her target. This bonus to attack and damage rolls is 1d6 at 1st level, and increases by 1d6 at 5th level and every four rogue levels thereafter. She also adds her Dexterity modifier to such a target. Should the rogue score a critical hit with a precision strike, the bonus damage is not multiplied.
Skill Savant
It seems like a reasonable boon to skills, but you have presented it as a massive wall of text.
Capstone
Where is it?
For Precision strike it works against flanked targets not just targets flanked by the rogue. And yes non-level 7 fighters in heavy armor are vulnerable.
I agree on the formatting. I will try to work on that.
There is no cap stone. As you pointed out Precise Strike is very strong and so is Skill Savant. They get the cleric treatment here.