I've never been fully satisfied with the way my A4 has performed since I purchased it. The test drive just wasn't enough for me to find that out unfortunately.

I decided to get the APR stage 1 software update along with the new air intake. My car has had the top end rebuilt for the oil consumption issue and I just recently had the timing chain system rebuilt out of fear and some oil was actually leaking from that area. Plugs, PCV and one coil are new as well.

After driving some later model A4s while Audi was working on mine, I really dislike how mine feels which is why I went to APR. Under normal acceleration when the car was stock, the 1-2 2-3 shifts were often rough depending on where it shifted in the RPM range. It drops the RPM just below the turbo boost and then pulls hard nearly instantly when it gets in the boost range. I drive in traffic a lot so I feel this a lot. Driving in sport eases this, but I then have to remember to go back into D while I'm cruising.

After the APR mods I still have the shift issue, but now I have a new issue. I reached out to APR as my shop that did the update doesn't think there is anything wrong with the car. I'm hoping someone here can help too. Under light to mild acceleration, the car is not always smooth up to about 3k rpm. If I have the transmission in sport mode, the issue can last higher through the rpm range. Hard to describe the issue, and the shop I take it to claims it runs fine for them. I'll describe it as when under acceleration the engine pulses/surges. I'm not talking give you whiplash when it happens, but you can feel it and you can see the tachometer bounce. With the new intake, I can clearly hear it as well. The turbo is far more audible and the air being sucked in creates a whistle, but it's a very broken whistle sound when this happens.

It's like the system doesn't know how to supply the right air/fuel mixture or something. I always run 93 octane and that is what my apr programming is set to. It can occur no matter the outside air temp and no matter the temp of the engine.

Since I've done some major maintenance, I'm trying to keep this car for a long time, so I'd like to really enjoy it.

I should add that no codes have been thrown, so unless the tech cares to really find the problem, there is no computer help.

One common issue I can think of that I don't see you mentioning is the DV. I would assume once your diverter valve goes bad it would throw a code but maybe it's not fully blown yet. It would sound like you describe it - air escaping creating a strange whistling turbo sound + performance/hesitation issues of course.
Check the DV first (FYI I replaced mine with the Forge BOV - Blow off valve - for increased sound and to ensure low maintenance since this one does not have a diaphragm that can rip). I heard later b8 models don't have the diaphragm anymore either but you car could still have it.
If you are still having issues I would check MAF and intake for issues. You did say you replaced the intake - make sure all checks out (pipe properly connected and tightened? MAF clean? Air cone installed correctly? etc).

If anything major was broken you would feel it and your car would start throwing codes. Sounds like you might be chasing a ghost for a while...

Unfortunately I've never had codes thrown to set the check engine warning. APR wants me to get them logs so I think i'm going to purchase the wired vcds unit.

Thanks for the reply. The DV is something that has been tossed around by the shop that did the apr software and airbox. I don't have access to a garage, how easy is it to access the DV without a lift?