I'm only in act 1, so I can't say much, but I'd say your defensive stats are a bit on the low side. I wouldn't trust my dh far into act 1 even, and I have much higher resists and life regen (but only about half the dps). I'd say some sort of life regen (life on hit, maybe life steal, or life per second) might help, especially since you using backup plan, and not the healing preparation. I would also look at higher resists too: I would normally say that 140 is too low even for hell, but it seems you managed it fine. Still, if you don't have a lot of regen, then then I would suggest increasing resists to help stem the flow of damage. I don't think there's a lot you can do about armor- 3k seems about the highest you can get with a practical budget.
What is it exactly that kills you in act 2? Can you describe your deaths in gruesome detail? Might I suggest swapping out Cluster Arrow for Elemental Arrow + Frost Arrow rune? I've been playing around with it in place of Ball Lightning and I'm really liking it so far, just takes a bit of aiming practice... Snare Kiting really helps immensely. I've a lengthy post on act 2 [here]
As for act 3, with my current stats in that post ... things take too long to kill but they're very much prone to kiting. If you're dishing out 90k dps though, beginning of act 3 should be pretty great for you if you have a decent aoe spam shot like Ball Lightning, NT, or Frost Arrow. Try swapping Bait the Trap on Caltrops for Torturous ground as well.
I am not all that convinced that resistances for a ranged class make that much difference, the exception would be physical resistance, I have gone as high as 600 and now use 250 to 150. Melee classes have a mechanic where stats provide much better damage mitigation, why should I as a ranged class try to mimic that? I have tried to work with the class mechanic, boost discipline, stack dex, find/use the biggest dps bow and keep targets at a distance and hope dps is enough.
I rely on caltrops alot, so much so I use a passive slot that reduced damage of the targets for 3 sec as they pass thru them. Why? Well because the maps are confined spaces, once I run out of room going backward to contend with walls, mortars, invulnerability, frozen things, I am going sideways and around or I am stuck between walls, I will eventually get hit, I can survive just one hit with 47k life and that damage reduction helps. The phasing monsters are the worst and as elites they are a challenge, I find I rely on discipline pool to survive to use my defensive skills.
My biggest comment is to get rid of sharpshooter (or steady aim) for Grenadier (a 50% boost to damage due to 3 cluster arrows at a time). I run Loaded for Bear because it does more damage when I need it: when something fast is breathing down my neck (or the dumb invisible snakes). If you play mostly multi with a lot of melee characters then cluster is preferable. I play solo and normally I could care less about burst dps when I have the jump on a baddie. I also abuse the crap out of Jagged Spikes. It is nice to do damage behind you and while you run away, very effective with loh for reflect damage mobs (i switch out weapons for them).
Shoot for about ~300 resist all and 35k HP and you will be able to fare a lot better in Act 2. 3k armor about the minimum, too, and is hard to boost. Run the enchantress if you want 15% more. Once your defenses get higher, switch out Backup Plan for Battle Scars because 60% of your life now is a lot more EHP and definitely worth it.
Your dps is nice, anything above 35k makes act 1 really easy and act 2 farmable. I haven't spent much time in act 3 due to my dps only being in the 35-40k range, so I have no comment on phase beasts.
Because of all the mob types that can avoid your attacks and 1shot you like the Lacuni or Writhing Deceivers (invisible snakes):
Unless you can double your damage to at least 150k, then killing them before they kill you is next to impossible.
And even if you DO hit 150k damage, you're still going to die a lot to random ranged attacks that you don't see or getting walled in bad spots, etc...
I have 45k hp, 1200 life on hit, 3500 armor, and ~350 all resist and special Deceivers STILL give me trouble.
They really just hit WAY too hard compared to everything else in the act.
But it's MUCH less frustrating than it used to be when I was gearing for high crit damage and using sharpshooter.
If I avoid the champ Deceivers, then I can farm the rest of Act2 without much issue.