I would definitely plug in a code reader. If you didn't do a PPI, it's very possible the dealer pulled the MIL bulb.

What you are describing, symptom-wise, is that the engine is experience serious misfires and the ECU is shutting down one or more cylinders to prevent damage. That would explain both the power loss as well as the pulsating.

That said, with your additional symptom, I think you at the very least have to replace the fuel filter. When they become clogged they strain the pump and that whirring/whining is just how they sound. (Of course they also sound like that when they are failing.) The fuel filter is inexpensive and easy to replace (though if you don't have clic clamp pliers you'll need to cut off the factory hose clamps and replace them with conventional worm-gear type).

So, to summarize, I would scan the car for codes, and if they are just misfire codes (in the P0300-P0306 range) then I'd replace the fuel filter. Oh, the heck with it, I'd replace the fuel filter regardless.

If you have codes other than misfire codes post them and we'll lend advice. You can go to any autozone store (outside of CA) and they'll read codes for free, but I'd recommend buying a basic code reader, like the MS-309, about $20 at Amazon, it will read and clear your typical OBD-II codes (MB specific stuff you need much more, but that's true with any make anymore).

In the meanwhile, I would stop driving it at least until you get the filter replaced and the codes read.

Good luck.