Just got it back together, and now it's idling very rough

[MPWR]

I changed the starter motor by removing the intake. Second time I've taken the intake assembly off (the first time was a cooling system rebuild a few years ago to replace those plastic pipes).

Got it all back together last night, and started it today. Started right up (yay new starter!)- but the engine died at idle. Giving it some throttle and running above 1000 rpm it behaves fine. But coming off of the pedal and letting the throttle close fully the engine is running very rough. Early in the day it would die as soon as the engine idled. I drove it around some, and now it does not die at idle- it just idles very rough.

CEL codes show both knock sensors flagging. I've cleared them several times, but they come back whenever the engine is run. Once today after driving it a bit I saw misfire on cyl 3- but after clearing I haven't seen it again.

There was a fair amount of crud on the injectors, which I cleaned off as gently as I could. My current theory is that maybe I clogged one (or more) in the process? If so, maybe running the engine a bit today helped to clear the blockage, but not yet completely? Just a theory, but the best guess I have at the moment.

There's a momentary whistling sound when the engine is warm, when I let off of the throttle. Can't tell where it's coming from. Don't know if it's a movement of air sound, an electronic sound, or something else. Makes me think maybe a vacuum leak? But I have no idea where- I've checked everywhere I can think of.

Stuck, frustrated, not sure where to go from here. Would appreciate any thoughts.

[spidertri]

Accidentally switched the throttle and cruise control cables where they attach to the throttle body?

[MPWR]

No cruise control on this one- only the single throttle pull cable runs to the throttle body lever.

[1996 328ti]

Sounds like my car and vacuum related.
Doesn't smell like fuel is burning rich, does it?