I bought a used, "pimped out" version of Frank's integrated early last summer. Its a good piece of equipment and would drive SongTowers pretty well. However, I turned mine in to Frank and got the Insight EC and a double 440 (I was going to drive HT3's but I ended up with HT2-TL's). I also have a double 240 and double 240/3 attached to my SongTower home theater. I also have that Parasound 2100 you mention. I only mention these to give you a background for my comments here about the different gear you mentioned.
Quite honestly, in a strictly 2-channel setting with SongTowers, I think a double 240 is perfectly fine. I listen to mine at good levels and the amps keep up no problem. Some guys may want more headroom or power, and so you could move up that chain as you feel appropriate, but I wouldn't discount his best value amp considering how much current it moves with the double die upgrade.
I also think that if your budget allows, I would move past the Parasound preamp into an AVA line to match your amp. I have the Insight EC and its wonderful. If you don't need/want the extra buttons/functions, the SL would be exactly the same sonically. The Parasound 2100 is a great piece of gear in a home theater environment, it has pass through, 2 sub connections, and an mp3 input jack. It also sounds very good and is cheaper than the AVA stuff. I prefer the Insight EC myself, but if MP3 jack was a need or lower cost was a limiting factor then the Parasound would be perfectly fine.
Of the two options you mentioned I would probably go with the AVA Integrated. I love separates, but the Integrated has two main advantages over the Emotiva kit.
1. Its an AVA piece of gear and the build quality, customer service and sonic quality will be 2nd to none in its price range.
2. AVA gear will last a *long* time and selling his gear on the used market is not particularly hard if you ever want to move up.
I looked at Emotiva long and hard before I went with AVA, the low prices and deals were almost too good to pass up. But in the end, I'm extremely happy with the AVA stuff. It really came down the personal service and record of quality. I think overall, Frank wins on both counts, although Emotiva does have its own following, but there are quite a few complaints out there and they still strike me as a relatively big box kind of place.
If it were me, I would skip the $1400 or $1500, get a double 240 and an Insight SL for $2000. It gives you the most upgrade flexibility, quite a bit of power for SongTowers, and AVA quality/longevity. I wouldn't be surprised if you didn't swap anything out for 10 years unless you really had an urge to play at ear bleeding levels.
As far as cables, that Blue Jeans recommendation is on par. Best cable out there for the money. Although if you need a bunch of them (I was hooking up a 5.1 system and 2 channel system all at once) it gets expensive. So I also have a bunch of Tartan cable interconnects (same company cheaper, precut line to compete with Monoprice). No complaints whatsoever, great cables whether you buy the lowpriced line or the the top of the line.
www.bluejeanscable.comwww.tartancable.comAs far as "are the differences hearable in amps/preamps/cables". Depends on the person. My dad listens to computer speakers and 128kbps mp3's and he generally couldn't tell you the difference between any of them. He would probably notice a pre-amp switch out. I can notice differences in the preamp, and maybe between a really crappy amp and a good one, but not so much. I just don't believe the amps change the sound a whole lot, given that two are putting out the same power levels. And cables, no difference at all. I make sure to spend a bit to get good quality cables, but I don't go overboard.
And your last point, its not a mistake, but maybe ill-advised. It would probably have a good sound, and many people could be happy with it. I like the synergy of keeping the brands the same though, and Frank makes one of the best.