About five years ago, I had violent shaking, shuddering and the blinking SES light whenever I'd accelerate too hard (such as going up a hill), and for me it was a combination of clogged CATalytic converters (that initially never produced any error codes, such as P0420 and P0430...they came later), fouled sparks plugs and two ignition coils that were going bad and producing misfires (again, inititally I had no error codes). And, sadly, the start of a failing CVT. I drove another year with that transmission after reducing my CAT problems and changing out all six spark plugs and ignition coil packs.
While trying to improve things, I noticed the car would drive better in Ds mode, provided I didn't push down on the pedal more than halfway. I'd start off in D, start up the hill, then drop it into Ds mode (which increases the RPMs), and I'd feather the gas pedal a little until over the hill, then I'd drop it back into D. After about 10 months, I could hear a piece of metal clanging around in the transmission, but I kept driving while I located a used CVT. Found one, and I've put about 165,000 miles on it.
While I have gotten the blinking SES light whenever I kept the RPMs at or over 3000 for more than four seconds (and the car would choke, sputter and shake) and then I'd have to pull over and stop, restart, etc...I don't get that problem anymore because I've adjusted the way I drive. Simply put, keep the RPMs below 3000 while going up a hill. You should be able to make it up most hills with 2800 RPMs, unless you're trying to go up it too aggressively. You can go above 3000 RPMs very quickly for a burst, then back off the pedal to bring them down to 2500 or so, etc.
You may not have my exact problems, but they sound very, very similar. Not sure if doing the D-to-Ds mode thing is what made the tranny go bad, but I haven't used anything but D mode since, and I'm at 280,900 miles now.
EDIT: BTW, in my case, the air duct intake hoses are intact and crack-free, and are not the cause of my acceleration problems when I go over 3000 RPMs for too long. However, today, as coincidence would have it, I went to 3500 RPMs for about five seconds, and MO acted just fine and zipped up a hill without any problems or blinking lights. In fact, I just posted abour that earlier today. Point being, you may have cracks and tears in your hose/boot that's causing your particular issue, since it's a common occurrence.
