I need some help with my Khajiit Assassin. I can't figure out which perks to pick and armor/weapons for endgame.

Skills:
Sneak
Light Armor
One-Handed
Picklocking
Archery
Smithing
and Restoration, for at least skill level 30.

As for my weapon set up, dual daggers for sneaking and dual swords for offensive.

Any tips on perks or weapon set ups? Armor too.

Silent Roll is actually really good, as you can move faster by rolling and it doesn't ruin your sneak as long as you don't run into someone.

I'd recommend maxing out the Sneak tree (Shadow Warrior is optional)

Also maxing your One-Hand will give you a great advantage. I'd also get the zoom perk for archery, as it's good.

As already mentioned maxing out on Sneak tree is highly advisable, but as for One-hand tree I would only max out the first perk (100% increased damage with one handers)
Smithing is also something you want to max out and take the daedric route of perks to get a couple of daedric daggers, as for the rest of your gear I suggest wearing the shrouded gloves you get when joining the dark brotherhood.

You will mostly rely on oneshotting everything with backstabs, but if you plan on actually doing the main quest then a pair of swords is advisable for dealing with dragons as is some profiency with bows, in this case you might aswell pick perks that increase your damage output with swords, most important are Dual Flurry and Dual Savagery.

Well, starting with the obvious, you need the entire Sneak tree.

I've only put one point into Light Armor because as an Assassin, whose job it is to attack from the shadows, I very rarely find myself getting hit enough to raise my skill in Light Armor, and dumping buckets of gold into light armor trainers is stupid in my opinion so I just avoided it. The perks seem really good for it, I just can't imagine a scenario in which I'd ever be able to level it high enough.

My character is an Archer Assassin instead of a blade assassin type though, so I'll be doing half of the Archery tree (ignoring perks like Ranger and Hunters Discipline that I don't find to be all that worthwhile), but you would obviously go more for the One-Handed tree since you use primarily swords and daggers. Although I do recommend that you put at least a couple points into Archery especially for times when you're in a situation where you've got a room full of baddies and need to pick a couple off so you're not overwhelmed by numbers.

Speaking of being overwhelmed, I also suggest that you focus on some Illusion Magic. The ability to Fury, Calm, and Fear enemies so you don't get overwhelmed is incredibly valuable. Us sneakies just don't have the ability to stand there and go toe-to-toe with a group of attackers, so being able to turn them on one another is a huge addition to the arsenal.

If you have any interest in using the Bound Bow or the Bound Sword then you'll only need 2 perk points into Conjuration, one point in the very first perk of the tree called Novice Conjuration, and one point in the Mystic Binding perk which grants damage bonuses to Bound Weapons.

Alchemy is always good for poisons and health potions but you said you use a little bit of Resto for that so you could probably get away with not having to worry much about Alchemy. There's such an abundance of Health Potions laying around in the world though and for sale that the only thing I choose to use Alchemy for is to make poisons for my bow shots.

Really it just depends on your playstyle. You know what you do and use the most, so therefore you should be able to determine which perks suit you the most.

I just hit Level 40, and this is my current build just to give you an idea on things I personally find helpful due to my playstyle.

http://skyrimcalculator.com/#9375

for much more enjoyable playstyle. i would drop archery and add illusion, as soon as you get to riverwood get muffle sound spellbook to help sneak up behind enemys and assanate them, calm and fury help too... use warrior stone, not theif or your stealth will outlevel your onehanded and leave you a little weak in the melee dept.. this way you keep your dmg higher. with this playstyle i sneak up on all single targets and assasinate them.. when multiple targets i usually use fury on one and watch them kill eachother or join the frey once they start attacking eachother by sneaking up and assasinating them. if you come accross an enemy that is hard on you, you can use calm on him and give yourself time to heal back up. once your illusion is high enough, head to the college of winterhold and buy invisibility spell(expert lvl spell i think) and then your really having fun, you can pretty much sneak up on whatever you like.. i spend my attributes like this. 2 health/1 magika/1 stamina. i put my perks in stealth as i can and max it... i follow the right side of the illusion tree to get silent casting and go one above that so illusion spells work on higher lvl of all types of enemys. i put points into light armor when i have perk points to spare.. one handed perks come as a last priority, you wont need them much if you take my playstyle and use this equipment, shrouded gloves for double backstab dmg on top of stealth backstab multiplier, you will be doing x30dmg from behind, assinating stuff left and right.. but i did invest in a few onehanded perks from time to time, on the right side of the tree i got the perks to speed up duel weilding. also up the middle i went for the perk that makes power swings cost lower stamina... sorry for all the typing, i just really enjoy this playstyle. also if you dont know, hold the left hand powerswing and right hand powerswing at the same time w dual daggers for cool power swing animation. even if you dont go this route, i still highly suggest taking the warrior stone at start of game rather than thief to keep your dmg up.

EDIT: house stark !! i notice your post after posting this myself.. how do you like using bound weapons, i wanted to do this but wasnt sure about it. im almost lvl 20 and havent invested in conjuration but am thinking hard about doing bound daggers. is it worth it and will it work as good as having chanted daggers like blade of woe? thanks mate... edit ... ugh i see there is no bound dagger spell on the wiki, that stinks if true.

for perks http://www.ign.com/builds/the-elder-scrolls-5-skyrim?d=000000000000000000000000000000000000000000000000000000000000000000000000000000000050001110010000100000000000000000000000000000050110103215111023005111000005111005111111100000000000011100000111111

stats 50/50 health/stamina

leaves u w/ 6 perks left to choose

lockpicking is too easy esp if u have locksmith gear, restoration is less effective than alchemy for healing imo