Hi! Welcome to the forum!
First up, I want to compliment you for doing your research, going out and listening for yourself, and still having the self-control and wherewithal to double check and ask BEFORE you buy all of your new gear!
What I will say in response to your questions is that I don't have any particular problems with any of your selections. If those are the products that you really want, they are all good products and there is no reason to avoid any of them. What I can provide though are just some suggestions for alternatives. My suggestions are simply what I would likely purchase myself, given the same sort of budget, room size, desires and content sources. So don't think of my recommendations as being "better" or any sort of "slam" against the products you've listed. These are merely other options that you might like to consider after I've explained why I might choose them myself
1) I might opt for a full surround sound A/V Receiver rather than the Marantz Integrated Amp + Schiit DAC. I have a few reasons for this:
a) the Marantz PM6004 is strictly analogue (hence why you added the Schiit DAC to your list, I'd imagine). While it sounds as though you plan to use your computer for 100% of your content sources at the moment, it is easy to imagine wanting to add other sources in the future. Maybe a video streaming box like a Roku, Apple TV, Boxee Box or the like. Maybe a TiVo or Cable/Satellite DVR. Maybe a videogame system. Or maybe just plugging in a iPod or smartphone directly via USB. My point is, it's nice to have the inputs available for such options
b) While you are focusing on getting a good stereo 2.1 system for now, you mentioned that you might be moving into a larger house in the future. It might be nice to have the option to expand to full 5.1 or 7.1 surround sound.
c) the easiest way to set up any A/V system is to have everything just plug into the receiver. The receiver becomes the "hub" of your system. It handles all the audio and it does all the switching between sources. A full A/V receiver will make this easier since it will handle both audio and video. Everything plugs into the receiver and one HDMI cable sends the video to your TV. Simple
d) you will get proper bass management plus auto speaker setup and automatic EQ and room correction. This is a pretty big deal! With the Marantz Integrated Amp, you have no bass management. You would end up sending full range signals to both the speakers and the subwoofer, which is far less than ideal. You want the low frequencies to be filtered out from the speakers and sent to the subwoofer instead. And having EQ and room correction can be a very nice feature that the Integrated Amp lacks.
With all of this in mind, and also considering your price point, I would purchase an Onkyo TX-NR709 7.2 A/V Receiver rather than the combo of the Marantz PM6004 + Schiit DAC. Pay close attention to the exact model number. There is a newer TX-NR717 that is actually worse! So you want the "older" 709 model.
There are a few reasons why I recommend the Onkyo TX-NR709 in particular at this price point. Mainly, it offers Audyssey MultEQ XT auto-setup and room correction. This is one of the best auto-setup and room correction programs and it also measures and EQs bass frequencies, which is very important. The 709 is also the least expensive receiver that offers full pre-outs so that you can add separate power amplifiers in the future! While the 709 has plenty of power for just 2 speakers in your fairly small house at the moment, in the future, you might have a larger room and you might want to expand to a full surround sound setup. The 709 is ready and able to run in full 7.2 surround sound at any time, plus it allows you to add more powerful, separate amps if you ever want to, which is rare at this lower price point, but an excellent option to have IMO.
You can easily plug in any source to the 709. It has HDMI ports, digital coax and optical ports, analogue stereo ports and you can even plug an iPod or iPhone directly into the front USB jack, so it's easily ready for any source. It can also connect to your home network with Ethernet and access many streaming audio and Internet radio services all by itself! So you have many, many more options to play around with
2) I happen to like most Paradigm speakers, so I've no problem at all with the Studio 20 v5 bookshelf speakers, especially since you've auditioned and liked them. That said, I will merely suggest a potential challenger The Ascend Acoustics Sierra-1 bookshelf speakers with the $300 NrT tweeter upgrade.
With the tweeter and crossover upgrade, the Sierra-1 are about $1100, which is close to the Studio 20 v5 MSRP. The Sierra-1 with NrT tweeter are, IMO, among the very best speakers available at that price point. The NrT tweeter is excellent, and a cut above the price competition to my ears. Very extended, very linear and accurate, but what puts it over the top for me is its excellent transient response that allows for better delineation and detail in the attacks and decays of notes. It's a tweeter that starts to approach the detail and resolution found in ribbon and beryllium tweeters, but at a significantly more affordable price point.
Like I say, I quite like Paradigm, so this is merely an alternative. But it's how I would spend MY money is all If it were the Paradigm Signature speakers with the beryllium tweeters, it would be a different story, but the Paradigm Sigs are in a different price bracket. So at this price point, I think the Ascend Sierra-1 w/ NrT tweeter are winners. If you go with the Sierra-1 + NrT, choose the "Natural" or "Dark Cherry" finish. They are GORGEOUS
3) I love SVSound's current lineup of subs. I won't steer you away from the PB12-NSD. It is very linear and accurate. Has great, strong extension right down to 20Hz. Perhaps what I like best is that it remains linear and keeps that deep extension even as you crank up the volume! That is rare among subs and basically unequalled at this price point. It is also "unbreakable", so even in a larger room in the future, it will be ready and able to handle it.
The only possible quibble is that it does not offer any tuning options just the one port-open 20Hz flat tuning. But if you get the Onkyo TX-NR709 with Audyssey MultEQ XT, that can EQ the bass, so having timing options built into the sub itself is less crucial. That said, if you want tuning option, a very good alternative sub would be the HSU Research VTF-3 MK4. That's a larger sub physically, so just keep that in mind
4) As for music files, ripping CDs to a lossless format like FLAC is good. I do the same. Although I make 320kbps AAC versions as well for my iPhone since space is limited on that device. Honestly, I have a heck of a time telling 320kbps files from lossless, but if you have the storage space, FLAC is 100% true to the original.
If you want to buy lossless downloads of music, check out HDTracks.com. You can download completely uncompressed AIFF files, lossless FLAC files or high quality lossy 320kbps files from them
I'm not really up on all the various streaming audio services, so I'm afraid I can't help you there. However, like I mentioned, the Onkyo TX-NR709 can access several online services directly by itself if you connect it with Ethernet. And with your computer connected, you could basically try anything you like and just cancel your membership after the trial if it doesn't float you boat
Hope that helps! And best of luck in your purchases!