Your room isn't large by any means so I don't think you need to worry about getting the most expensive subwoofer on the block. If your budget truly is $1,000 for a receiver and speakers, I agree that more of your money should be spent towards the sub.
I wouldn't spend $250 on the E-300 if I were you. Consider that the E-300 does not have traditional speaker terminals so that means banana plugs are out (I like em for faster unplugging and such...your call!). But the E-300 can be had for $209 w/free shipping from Denon directly or $189 from accessories4less. I don't think the E series sold as well as Denon hoped because this series is cheaper than the xx13 series.
If you want to bump up in calibration quality, the Denon 1713 (which I prefer over the E-300) can be bought for $275 from accessories4less. You could also argue to purchase the Denon 2112CI for also $275. It has 7.1, analog to hdmi, and also MultiEQ XT. Just a thought!
For speakers, you first have to decide between bookshelves and towers. There is no clear winner with bookshelves vs towers as everyone has their opinion once you include the subwoofer into the mix. But, you will get more money out of a bookshelf compared to a tower. Fewer drivers, smaller enclosure, smaller price
With a budget in mind and bookshelf speakers I vote for the Polk RTi4/RTi6, Infinity Primus P163, Pioneer BS-22, and Cambridge S30 (I couldn't get the cambridge because I just can't stand the look of em).
If you want/need towers at a fair price, I think your options boil down to the Pioneer FS-52, Cambridge S70's, or the Polk Monitor line. I think the Pioneers and Cambridge outperform the Monitors, but sound is largely subjective so your call. The Polks and Pioneers will be at your Best Buy so audition for 15 days and see what you think.
I own the Pioneer FS-52 and center channel to go along with it, and it blows me away considering what I paid at sale price. They go on sale for $87 per tower, $70 for the bookshelves and $70 for the towers.
If you got the Denon 1713 or Denon 2112CI for $279 (and I actually would spend $30 more to get the 2113CI or $20 more to get the X2000), the Pioneers at a sale price for $244, you have $500 left in your budget for a sub. I also own the Denon 2112CI.
And yes...I would get the SVS-PB 1000. Your wife will give you "the look" regardless of what you get.
Over and out.