Definitely consider 6 S38 speakers instead of 5 plus a "center channel" speaker. No center channel speaker could possibly be as good a sonic match to the S38 as another S38. The S38's horizontal stature makes it an ideal candidate for use as center channel speaker. This should save you money as well, since the S38 is (I presume) only sold in pairs due to its L/R mirror-image design.
I was planning on purchasing 6 S38s, but keeping one as a spare or for future 7.1 setup. You really think the S38 in better than the S center-channel speaker?
Looks like a nice setup, the subwoofer isn't the best but if you don't have the extra cash it isn't a bad choice for the price. IF you can spare a little extra money look at something more like a Polk, they still aren't that great but they deliver alot of bang for the buck and it's a little more defined I think.
I would think that identical speakers all around are probably the way to go. Then use whatever money is left to buy the sub. Of course, that is with the understanding that you'll want to upgrade the sub at some point.
My philosophy for components that I know I'll upgrade is to get the least expensive one that I can live with during the interim. Then I don't lose as much when the inevitable upgrade comes around. The Sony sub that you chose will probably fit the bill. I have the AWM-40 in the travel system and it never fails to wake the neighbors.
I would say devote a certain amount of money to the sub. Just try to squueze a nice $300 sub into your budget and usually you'll be alright unless you get top-end floorstanding models which will pump out more than the sub can, although that shouldn't be a problem anyways.