I don't know about the Cobb's capabilities. I have one but it's just for a back end flash for fueling so I don't really mess with it much.
I've never really had the "strong throbs"
but I will say it wasn't until recently that I got my car running pretty smooth. It was always pretty smooth between 2k and 6k..it was down low and up high that the inconsitancies would show.
I too bought mine use at 25K (it has 30K now) and it took me a while to work out the bugs. Frankly I'm still dialing it in...but probably always will be.
Driving it as a stock car initially it was fine and nobody probably ever would have noticed anything. But the minute I started putting power to it...the short comings appeared. I had noticed among other things a slight stumble at low rpms and showed as misfires at high rpms. Those were also caused by a few other things that I slowly worked out. Plugs didn't help the slight misfire...but I will say, since you have just had your plugs done...one of the things I did to the Bosch BMW plugs was to regap them as I had found they varied a bit, .035-.04ish IIRC. They are all at .030 now. One of the other things that helped...a good flushing of the fuel system. I used Redline SL1 and added an entire bottle to the tank with a gallon or so left in it. I then immediately drove that out keeping it to under 3k rpms and circled the gas station until it indicated just a couple miles remaining. I did that at the end of 2 consecutive tanks of fuel. That was one of the most notable differences I felt in my car as far as making it run smooth. Other things of course have been a leaky injector I found (in hindsight that was apparent in cold starts), the carbon cleaning I did (nothing huge there but still needed), and really just kind of going through the car pretty thoroughly as I had no idea what kind of fuel the previous owner put in the car just that the scheduled services were done.
Some of my stuff doesn't necessarily apply to your situation but the minute you start trying to run more fuel and air through it(aka power)...if anything had been neglected..it'll show up, or so I've learned. Now I'm pretty anal and meticulas about everything.
One other thing...don't know if you have access to any coding tools, but if you can get in to the error logs in INPA, I found a fair amount of errors in there that I cleared out. Not sure if they all showed up as codes through other means or not...not thinking so and I know they weren't currently showing anywhere but were in there. (that would worry me if I were under warranty)
Good luck getting it sorted out. Some may say it's normal, I'm not so sure of that...guess it all depends on your definition of "normal."