Noise & Muddiness in Amplitube 4

[season5]

Rig: custom Stratocaster with HH pickups > 5 ft. 1/4" cable > PC (Windows 7 64-bit)
Amp: MesaBoogie DualRectifier
Cab: Ampeg 8x10, Mesa 4x12

Okay, so like a lot of other people I have been dealing with a lot of noise coming into my input signal.
To help clean it up I'm running an Dime Noise Gate (45Hz, slow release,) an EQ pedal, another Dime Noise (214.2Hz, fast release,) another EQ, and a compressor as opposed to Amplitube's built-in noise gate that left in a lot of noise and made it almost impossible to get the tone that I want. Now that pedal chain does help reduce the noise significantly, but I am running five pedals and I feel like the low end is still a bit muddy.
Also, anytime I go to adjust the volume or use the killswitch I get pops, static, and signal disruption.

The pickups I currently have are some cheap ones that came in a wired pickguard I ordered from China, which were much better than the single coils that the guitar came with. I'm not positive of the magnets inside the pickups but if I had to guess they might be Alnico 5s.

I've been thinking of swapping the pickups in the hopes that they might help reduce some of the interference, in addition to giving me a better tone. I'm waffling between the Seymour JB/Jazz set and the DiMarzio PAFs, however my bass has active pickups. I still get noise, although I'm not running quite as many pedals to clean it up. Someone feel free to correct me but I think because the pickups already have power going to them they don't suffer the same issues, especially since the signal doesn't break up when I adjust the volume.
I've also been toying with the idea of swapping out the volume and/or tone pots to see if that makes any significant difference.

So my questions are as followed:
1. Is there any (free, ideally) plugins available or tricks to help reduce the noise and static issues without adjusting the hardware of the guitar? I've seen a few different options but I'm not sure what would be the most reliable.
2. Active or Passive pickups? Personally I prefer passive because I'm not doing anything super shreddy (I'm not that good a player) or playing in low tunings to need that sort of thing, but if active pickups can help my situation while giving me the sound I'm aiming for I'll give it a go.
3. Volume pot, tone pot, or both?

[Peter_IK]

What audio interface are you using? You mention 1/4" cable and then your PC. AmpliTube works best with a proper audio interface with Hi-Z/Instrument input. I will bet that has a lot to do with it.

[season5]

None. The cable I have is using a 1/8" adapter and plugged into the mic jack in the back of my desktop. I've been looking into used interfaces but between that and replacing the electronics in the guitar I'm leaning mostly toward acquiring the latter.

[garfy]

The cable I have is using a 1/8" adapter and plugged into the mic jack in the back of my desktop

Sorry DimePictures, Peter_IK is correct on this one then. The mic input on the motherboard is not designed to receive signals from guitar pickups and so this is why the signal in AT4 is not as you would want it.

replacing the electronics in the guitar

This would not solve your problem I'm afraid. Getting a clean and appropriate signal into your PC can really only be achieved using a proper audio interface.

There are reasonably priced interfaces from Focusrite, Tascam and M-Audio (all probably cheaper than replacing pickups) or you could look at IKM's AXE I/O for something a bit more up market.