I highly suggest you do NOT port the TB or MAF, it gains nothing, can cause surging, confuses the PCM and is a waste of your money. In 100's of cars I tuned that had some air porting the end result was the engine ran better when customer put the stock MAF, airbridge and TB back on.

As to CAM, do a search here on forum to find content about CAMs but being you have a A4 and it functions best with the correct line pressure and engine vaccum. I'd suggest not going lower then a 114 LSA else the loss of low end vaccum will effect the low end, idle and shift points.

Yes you do need a bit larger injector, I suggest the SVO 30 which Ford spec'd for their racing but they are the same brand as what C5 uses but with our higher fuel rail pressure they are 36 lbs/hr over your stock 26 lb thus when needed the SVO 30s can flow 30% more. You can buy them new for aobut $215 a set and only take you at most 45 minutes to do the swap.

Since you have a Blackwing you might look at the Icebox which is a cold airbox for the BW we designed and sell.

Also to make all this work well together and perform well I suggest a custom performance tune which is our main business. With a true custom tune you'll see good overall performance gains of HP and Tq but also the A4 will shift better and engine will run smoothly over all engine RPM/load and conditions.

Porting your stock heads will be just fine with also better valve springs to allow a bit higher rev limiter setting.
You might consider having your PCM flashed as example with a 2002 Z06 ( my '99 Mallett 435 LS1 has a 2003 Z06 flash) calibration and switching to a STOCK 01 or newer 85 mm MAF to match the bit more flowing intake manifold. This then assures the larger MAF fits GM's model within PCM as to correct airmass and grms per cylinder

As it is now with the changes you made really require a good custom tune

This you could do for less then 5K.