When I tested the premium system there was plenty of low end bass. I noticed a slight (to my ears) weakness in the mid-bass but it was much improved in comparison to the low end (stock) system. The stock system is very bad IMO. I spent a half hour listening to the stock system and trying to convince myself it was "good enough" and finally ordered the premium. Since you say you can hear nothing below 800Hz I'm assuming you are talking about the entire low end and not just the mid-bass?
There should be two sub woofers, one under each of the front seats. I believe they have their own two channel amplifier (why a two channel sub amplifier is a mystery to me). Is it possible that these aren't working (from the head, the amplifier or maybe a fuse)? Since the rear speakers are larger perhaps shifting the sound that way helps restore the missing (
) subs and the combination is what is causing the various sound issues?
In any case I'm not sure how you wouldn't have noticed the missing subs before now so I feel stupid mentioning it...
The $1900 is to upgrade the sub amp from 40 to 70W, regular amp from 25 to 40W (I think it also adds three extra channels) (IIRC), to add the extra speakers and to upgrade the speaker quality. The system isn't overly great but I did some research and I didn't see how I could spend less than $1,200 (probably more) and many hours of my time installing a better system.
I'm sure someone will speak up at this point who can do it cheaper and much better but he knows more than me or is talking out his ass and I do not want to spend $500-$1,000 just to figure out which. I don't think the premium system is a $2,000 stereo system but I think it's cheaper than the alternatives if you place any value on your time (for research and installation) and you'll wind up with fewer fit and finish issues long term (and therefore less "system noise" if you want to look at it that way).