Question - not really sure how to title this

If you are overshooting the temp (daisy wheel off and running for 30 minutes), then your egg is running hot with a large good fire. This fire is well above the 375 you say you want to grill at (a low temp in my book)

But then throw on the daisy and choke the lower vent? Well now you are slamming on the brakes. This chokes the fire back. Your smoke at this point is foul and the product of incomplete combustion. The fire isn't being magically made to sit at 375. It is in death throws and can only MANAGE 375

if you add the meat any time soon after choking down, it will collect all the soot and foul smoke that this poor fire is throwing off

No need AT ALL to let a fire get going hotter than it needs to be and then choke back

I'm also thinking that using a powered draft unit *might* be contributing to this too. If you have slammed the brakes on the fire, it will be starving for oxygen. Then you add the powered draft unit to manage temps. 

if the fan kicks on, that large pile of starved lump will raise temps quickly, because it is all lit and ready to go. It is a drowning man taking a huge gulp of air.

It rises more quickly than it might with a stable fire. Because you have a lot of lump that is already lit and will readily get hot with the fresh air. 

your fire is a large pile of lump, once all burning fully. Now it is choked back. The lump burning poorly (dull low red) and maintaining your lower (375?) grilling temp

a normal 375 fire would be much smaller, but burning fully and cleanly (orange white). Clean fire

Very quickly, when that fan kicks in, the temps probably rise past your set temp, because you have so much lit lump on the batter's circle. And so it takes off again. Oops. Overshoots, and so the controller shuts down to limit the temp. This chokes the fire again

really sounds to me like you are grilling the whole time with poorly combusted smoke

try using the daisy wide open to stay around 400. No controller

ignore temps from opening and closing the dome. Controller is confused by that i think. So don't you dall for it too. The fire isn't getting cold when you open the dome. Just the dome thermometer 

at 375-400 your lump is really 1000 or so and THAT is the temp you are grilling at. The dome temp reflects the temp the top of the steaks are being roasted at

You can keep the lid open the whole time. This means you are only direct grilling and dome temp is irrelevany

If all this is too confusing:

-lose the controller when grilling 

-don't drive the car at 100mph for a half hour to warm it up if you are only going to cruise at fifty for your trip (no need to get the BGE roaring for a half hour and then choke to 375)

-smell the smoke. If there's bad smoke coming out of the egg, it isn't ready to use