Thanks! So, on my list of things to look at, in order:

Air filter
MAF
Spark plugs
Coil packs
DISA valve
O2 sensors
Fuel filter

Intake boot was just replaced, and I was told that the dealer I bought it from did the spark plugs, but who knows.

Not hearing any noises from the DISA valve, and up until this weekend it always idled and ran smoothly as expected...BUT I have noticed that recently, when taking off from a start, occasionally it hesitates, then goes to feeling like I just floored it. So I will definitely check it.

I would check for vacuum leaks at the disa onring. 5 dollar fix. Then look at spark plugs if they haven't changed.

If that's it, is it possible to buy replacement seals from the dealer? Or should I get a kit like this one? Tried to find the parts on realoem.com but all I could find was the entire assembly.

RealOEM.com * BMW E53 X5 3.0i Intake manifold system

If that's it, is it possible to buy replacement seals from the dealer? Or should I get a kit like this one? Tried to find the parts on realoem.com but all I could find was the entire assembly.

RealOEM.com * BMW E53 X5 3.0i Intake manifold system

How many miles on your DISA? if over 100k I would just get the repair kit, its wonderfully engineered.

I have 70k on my car so my DISA is in great shape, I only needed to buy the O-ring seal for it (G.A.S. sells the O-rings separately on the website!), and I figure when it gets up in mileage and with some more wear down the line, I will install the rest of the kit and probably another new seal when the time comes.

You'll be able to tell if you have a leak at the seal, bc when you unbolt the DISA if you can pull it out of the manifold rather easily, its bc of the seal. You'll also notice it will probably be flat as all hell too, which I noticed. Kind of a pain to scrape the old one out but gave me some time to clean the DISA too. $5 fix. If you need to do the whole repair kit bc of age/mileage, its simple to do and costs 80. I'm thinking about getting the reduced pressure coolant cap from him as well.

No idea how many miles are on it. My X has around 152K so presumably it's been replaced or repaired at some point. Suppose I'll decide what to do when I take it off. So where can I get that seal if that's all it is? Would NAPA have it maybe?

Presuming thinking its been replaced isn't really doing much, not to be a dick. It takes 30 seconds to take the DISA off the car and test the condition of it, by checking the vacuum pot and seeing if the retaining pin is starting to loosen up (you DO NOT want that in your engine)

At your engine's age and mileage and given that you didn't buy it from an enthusiast, I would almost bet that the DISA is original, and at the very least the o-ring is toast on it and you need a new one. If it were me, I'd just pony up the $80 and do the whole repair, as I've heard some horrible stories of DISA's that have aged, subsequently fallen apart in the manifold and screwing up some major shit. Wouldn't you rather take it off the car real quick to see if its in good working order, before shrugging off the repair kit?

However, if you must do just the seal, its $5.65 shipped for O-ring from GAS, I presume you can wait a couple days for it to arrive in the mail?
Product M52-tu & M54 O-rings

Oh I do plan on taking it off, I actually edited my post to make that clear just as you posted that last reply :) Will post back with results.

Good deal man :)

Let us know how it looks! and read GAS instructions on their website, they make it very clear also how to test DISA function and visibly how a healthy DISA should look!

DISA valve looks OK. The seal could stand to be replaced, but it's not completely flat. And the air filter and spark plugs are somewhat worn (I'll replace them) but they're not abysmal. I'm thinking there must be a vacuum leak as the misfire is not contained to one or two cylinders. It's random...every time I pull the codes, it comes back with different cylinders. And now the O2 sensor codes are gone. Next thing I plan to check is the PCV system.

What I don't understand is, why does it only run rough when the SES light is on? Once I clear the codes or sometimes if the light goes off on its own, it's fine.