With that budget, you are much better off getting separates. I'd recommend onkyo refurbs (shoponkyo.com) for bang for the buck. Shoot for the 700 series, but go with the 600 series at the minimum.
The default answer around here on speaker around $1000 tend to be the SVS S series which you can get in a 5.0 config with an NSD 10 for around $1k shipped. I have not heard the SVS speakers.
This combo will rip apart anything you can buy in a box.
For other options, Aperion has a 5.1 set shipped to your door for $1k. I have heard the Aperions and like them very much, but the SVS do have better specs. Aperion will give you 30 days to try them at home, and if you don't like them, have them shipped back at no cost.
If you need to shave dollars off, the Harman Kardon (Harmanaudio)store at ebay is always a good source for speakers. Infinity Betas are getting hard to come by there, but you can still put together a 5 piece Primus set with large fronts for well under $400 (no sub). If you're patient, you could do the same with a JBL ES or Studio L, albeit with small front speakers (no as much of an issue in a subwoofer supported system).
I would not, however, buy an HK subwoofer. For the money, SVS, Elemental Designs, HSU and other Internet Direct companies can offer you an amazing value. I'll put in my vote for fellow Iowans ED. Their subs may not be the prettiest girl at the dance, but you pay for performance, not looks.
If you have a paradigm dealer near you, you owe it to yourself to give them a listen also.
At the end of the day, you have tons of options at ~$1000, and the only way to pick speakers is to give them a try. Subs are a little easier to buy based purely on recommendations, but speakers can be a very personal choice. I really like the warmth of my Aperions, but I love the brightness and clarity of my JBLs (even if silk dome folks might find them "harsh").
Any of these systems will last you long after you move out of the garage.