This will be long-winded since I just got coffee into my system.
Honestly, your biggest problem is your lack of experience with the other weapons. It's possible to win the game with just your chosen weapon(good luck with a pure scythe run though), especially with the well-rounded DS, but it's a lot easier and rewarding to at least try out the new gear you acquire as you go on. Not to mention, having three or four nice upgraded weapons gives you a larger playing field in terms of available combos and really how you approach encounters. I enhanced at least DS, Lunar and Claws periodically(they have something for every situation), but immediately tried to max Tonfas, Kusari-Gama(no one seems to realize how awsum that thing is) and Dual Swords, because that's just how I roll. Pick a few guns as your main and concentrate on kicking ass with them. Same with the combos, master a couple from every weapon(especially ones that you can link into the dreaded Izuna Drop, since you can't be hit while doing it) and leave the really showy crap for when you know you can do them safely.
A few things: Surviving in higher difficulty levels in NG2 is based on avoiding damage. That might sound obvious, but the fighting system is built from the ground up to avoid taking damage. Ruy has several "invincibility frames" in his animations, split seconds when he's invulnerable, and a lot of the combat against the official "harder" monsters in the game rewards you for taking advantage of that. For instance, the Claws, if upgraded note, have several combos where Ruy teleports around and spends a lot of time in the air and these not only serve as moments of invulnerability where incendiary shurikens, warlock fireballs etc can't hit you, but also give you a breather from the constant pummeling you face by making Ruy unreachable for the moment. The Izuna Drop is a prime example. And a really cheesy method against human enemies.
On Acolyte(hey, I started on that too, shut your face), you don't really need to dig deep into that system, but it helps to take the gist of the strategy to your heart. Pick an enemy and separate him from the throng with any quick combo of you choice(say, forward+x+x+y+y) or circle your enemies with constant dashes and rolls until some straggler charges, if you get a couple of good clean blows in, the chances are the enemy loses a limb and it's obliteration time. With wolves, for instance, if you keep circling a pack with roll jumps or just keeping your block up and dashing simultaneously(slow, but makes you almost invincible) you'll get a running attack by a new furry friend for certain. Now, another good tactic is to master the Wind Path, or the dash you can make immediately after blocking. It doesn't always avoid throws, like the Kuja tail grip, but if the attack starts with any blockable animation, hold your block and push dash immediately after the attack hits, a wind path towards the enemy will get you behind him most often. Pound into him, wind path again, repeat until the horde is on you and you have to change your chosen target and circle the group again. When a wolf does the running thing, wait till he's near and quickly dash to the side to avoid the running throw. Put a combo in and change the side with another wind path or a dash and keep hitting his back or side. Eventually an arm will fly off. Good, that wasn't so hard, right?
However, tight corridors pose a problem and really make you love every moment you spend in an invisibility frame. So, it's good that you got two things with the longest frames in the game: Ninpos and Ultimates. On ninpos, it's better if you stop thinking them as straight damage dealers, but tools. An unupgraded fireball makes you unreachable for as long as the animation lasts. When in a pinch, hit the ninpo buttons and savour the moment. Some boss attacks(like all the **** the lightning worm throws at you or the massive bone walker's annoying kicks) can be completely avoided with that. My fave nipo, The Wind of Blades(or limb rain) is the best combo against massing groups of ninjas and soldiers, since it delimbs just about everyone. Suddenly the battlefield is an obliteration fun zone, just as long as you avoid their suicide attacks(dash next to an enemy and push y, repeat, never run next to delimbed enemies). The flame phoenix ninpo makes foes lose their ready stances and interrupts attacks, which is a blessing with some demons. Black hole is a flyer killer. Forget about the ratings and go on a ninpo spam. The game will drop one or two chests in a level which always max your ninpo bar, since some of the chests only contain the essences you need at the time. Same with the essences that spawn. Ultimates on the other hand, are a bit more difficult to get off. First of all, once you see a blue or a red essence you don't immediately need(even a tiny one will start an Ultimate), keep your block on so you don't immediately use it(since Ruy only attracts the globes when your block is down) and dash into a position that will net you the largest amount of enemies but also give you a split second of time to suck the essence and start the UT by holding y pressed a heartbeat.
Most of the ultimates are separated into a couple of combos, which you may direct slightly. So once you are well into(say, 5 slashes) an ultimate, point Ruy into another enemy and so on. You'll get it. Now, a word of warning some of the first level UTs really suck. Especially Lunar only shines once you upgrade it the second time. It's ultimate ends with a massive expanding circle of fire(yeah, it makes no sense, "power of the moon" wut) that wolves really love. A real group killer, you'll love it.
Hang in there. And don't forget about the scythe, bosses hate it.