which components to buy?

Save some money and look into Emotiva or luck finding used gear, $1000 isnt going to get you into the party. You could get an Emotiva amp for your budget and use the Reciever as a pre out assuming it has pore-outs but in time going to a true seperate Pre/Processor will sound better.
List all you gear if you could...........things are way to vague to be of any real help.

Speaker Company = Infinity
Z9 = Pioneer?
RX3300 = Yamaha ?

Yes, as said before 1000 is definitely not going to go far! Good thing is if I'm remembering right the IL 60's have built-in subs with 500watt RMS amps. This should make powering the mids/highs a lot cheaper.

If I were you I would consider buying used. I got a great deal when I did the same... Outlaw makes some decent stuff but I would recommend breaking your budget a little and going with what makes you happy now instead of again upgrading later like me... or you for that matter. That said there is some used rotel amps that sound decent. 1075's and 1095's seem to be everywhere! You could always do something like a 1070 + 1075 for 7.1 and used the amps will cost you near 1000. Does your current system provide pre-outs? If so perhaps you could just get amps and wait for the pre/pro once you've saved up some more $$.

How do you feel about D-Class amps? I like the rotel line of D-class (I have two 1091's) but would recommend any of the other cheaper D's they make. Most like the 1077 better then the 1075/1095 rotel's but they are tough to find used. I read the 1085 1076 and 1072 all do great as well but again might be tough to find use although they are cheaper.

Slightly more money then rotel and parasound becomes an option for the amps but of course buying used. With powered subs a good used A23/A52 combo might do very well for you. That will be my next upgrade, some JC1's and an A51/A21's (when I get my B&W 802D's :-)).

Strangely enough Panasonic is making D-Class receivers along with at least one other company.

Google:

Sa-xr55 802D

Read review and see if that would help you achieve what you are looking for. I know it's not a pre/pro and it wouldn't be my first choice but it might fit your needs pretty well. There are a ton of options for receivers as well as bi-amping etc.

What is it that you are looking to get out of the upgrade that your current system can't provide? Have you thought about accoustically treating your room? Is it a dedicated theatre? Do you have a matching center for theatre? Do you use your setup for music? If so do you care about imaging and the sound stage or are you happy with just detailed sound?

Forgot to answer what to look for:
Power, S/N ratio, clarity, imaging, depth, how big of a soundstage it creates, what your source is, what am I going to plugin into this thing, how much space is it going to take up, the heat it generates, can I move it, what gadgets you need on the processor and most of all, listen to them! I know, the last one is tough when you live far away but it can be worth it.

One last peace of advice, yes monster makes some good sounding amps for a great price but be warned, many bad reviews on quality, longevity, and catching in fire. I would not try them ever!

One or two more things to look at. balanced vs unbalanced inputs. If married, what will the significant other let you have? Do I have somehwere to put all this stuff. Will this expensive equipment be protected from electrical problems (i.e. lightning/surges)? Am I going to be upgrading any audio/video that I already have that this might need to work with? Will I add blu-ray or other HD Audio formats? Do I need an EQ because of the room accoustics? Do I want it to control video as well? Do I want an on screen display or is the LED ok?
Again, most of this goes back to your goal and what you plan to use it for. If your room is untreated and you are having sound issues I would strongly suggest spending some of that 1000 to fix that problem before buying anything else. Room, speakers, and source (cd/tape/record/dvd) will be the biggest sound changes in your system. I say source only because a high quality recording CD will sould much cleaner then a low quality tape. You can try and fix the room electronically but it will cost you...

http://www.audioholics.com/reviews/acoustics/audyssey-multeq-pro-sound-equalizer

The best of luck!

$500 range newer receiver, with HDMI 1.3, Dolby and DTS Master HD capabilities, and Room EQ. Then, spend $500 range on used 5.1/6.1 channel amp - like used Parasound HCA1206 (run bridged for front 3 channels, minium). Other-wise, HCA 1206 running all around, or HCA 1205 for front 3 and side's.
This will get you the latest decoding, plus much much much stronger applification than what you'll get from ANY receiver's amplification - especially for your critical front L/C/R speakers!
Good luck

actually WHAT ARE THE DIMMENSIONS OF YOUR ROOM? At 1200 square feet, your room would be something like 20x60. Is that right? If so, I'd be looking at larger powered speakers likely - such as Definitive BP's with large woofers, to help drive the room.
Hope this helps