1. If you've built the enclosure to specs, filling is really not needed. But a bit of filling might make the sub sound better to you. You can use the "polyfill" used in Reliance Pillows if you don't want to use glass wool. From what I've heard, 350 to 400gms of polyfill per Sq.Ft (of enclosure) would be a nice starting point.
2. Did you also check the RCAs? Low-quality RCAs can cause whine. Running RCAs and power wires together can also introduce whine (may not always be the case with good quality RCAs, but doesn't hurt to check).
Now, this is unsubstantiated by personal experience, but I've lately been hearing of quite a few people complaining of whine while using GTA MKII Special Amps. If possible, please try substituting the amp for another one (maybe a friend's) just to check whether the whine goes away.
3. It is not that difficult to do the tuning. Just set the HU to 'flat' or 'defeat' (all boosts and cuts and EQ to off) & then set the LPF & HPF, depending on the capabilities of the speakers & sub you are running. If you have 6.5" comps/coaxials up front, you can safely HPF them at 80hz and LPF the sub at 80Hz. I think the HU will let you do this, or you can set the filters at the amp end. Once you set the filters, you can do the TA and then fine-tune.
BTW, in some HUs, using the 'flat' or 'defeat' setting first will disable the crossover controls in the HU. If this is the case with your HU, you will have to first manually turn off the boosts and cuts, EQ, loudness, etc etc. Or, you can set the HU to flat/defeat and set the filters in the amp.
Yep, you will need the measuring tape to set TA. Set the driver's seat a few inches to the front (from the position it is in when you sit in it) and measure the distances to the various speakers. If you're not sure how to enter the details into the HU,post the measurements here. There are quite a few folks using that HU here, so you will easily get help.
4. If you use good quality power wires, this problem should go away. For a GTA MKII, power wires of 8AWG should be quite enough.
All the best!
