Standard build? 3 DEX and no Chemistry for a Throwing build? 4 INT? Almost all of your skills will be penalized, except Guns. You'll be suffering in the beginning; by the time you're not suffering so much anymore due to all those penalties, your ability to shred enemies with ARs would have been nearly as great had you not min-maxed so much in the beginning. Without Chemistry (which there's room for in your stated load-out), you'll have little or no access to Mk IV or V grenades. You'll have to wait quite a while just to find adequate quantities of Mk IIIs in shops.
Chemistry should be your 8th skill, period. Later you could branch into Biology and eventually get it to 130 for the high-end stims and hypos, which will be very handy for an AR juggernaut. Again, having shit-tier DEX would hurt you because it makes fishing more difficult, even after the changes.
Trust me, that 9 CON and extra-high PER aren't worth having shit-tier Initiative, penalized Throwing, stunted crafting and Lockpicking/Hacking, etc. Put INT at 6 and DEX at 6-7, and aim for 50 Chemistry fairly soon, then 69 Chemistry when you can. That will carry you through to DC easily with Mk IV grenades (and mines, if you go that way). In the beginning and even through the mid-game, one grenade can decide many fights.
High CON is good, but 7 should be fine. I'd rather have two more points in STR than CON if I had the additional points to spend, because knife homos will utterly trash your AP and accuracy when you're just barely strong enough for your armor.
I've just played through nearly to DC with an assault rifle juggernaut, and I'd have killed myself by now if I'd set my INT and DEX so low.
AR juggernauts are extremely vulnerable to knife homos, 100% of whom have Crippling Strike and always use it (and it routinely stacks twice in a single turn for -4 STR;
Styg fix pls). I'd rather bomb the shit out of myself with a Mk V grenade then let a little knife homo anywhere near me. (It was the same story in my Early Access sledgehammer playthrough). They are also very vulnerable to psi, especially if you have low WIL, which mine does and yours will, too. None of your armor is worth a squirt of piss, and good luck resisting any of the disables. If you come upon a large group of psionics, be sure to use Morphine, because even with 700-800 HP and massive shields they can still trash you fairly easily (mainly thinking of Lunatic HQ here, or Tchortists).
TL;DR: Don't min-max so much. Dial down the CON and PER a bit and dial up the DEX and INT, and make sure you have Chemistry.
Oh, with a Guns guy, I'd go for Classic just because leveling up faster = more Guns skill, sooner = more accuracy, sooner. If hitting 25 before you reach DC is a problem for you, though, go Oddity instead. Pick whichever faction you like; their content is about the same as far as quantity is concerned. However, I suspect Protectorate has a better merchant. Still and all, slaughtering Fort Apogee is challenging and fun.
