Yea, building it yourself is no problem at all, you just need to read the instructions which come with the hardware, and there are plenty of online guides to help you with building.
Yea, the more fans in a case, the better. If they're too loud, you can buy newer, quieter fans for chump change. As far as the power source, most PSUs can hold 5 fans.
The DVD drive can be changed easily, you have a lot of oney left over, so you can check out other drives with better reviews. I was actually going for a cheaper drive, but I saw that this one had a lot of reviews and 5 stars so I just went with that one.
For SLI, two cheap cards are no use at all, theres no point with that. Some cheap cards don't even support SLI. The point of SLI is to pay for two cards to get ~175% the performance of one. Right now the 7800GTX and 6800Ultra aeren't too far from eachother in price, so I would go with the 7800GTX, but you don't have much money left from the $3000 budget. With the money you have left over, either stick with the 7800GTX or get 2 6800GTXs. Personally, I would go with the 7800GTX, even though I was recommending SLI earilier. Again, I'm no hardcore fan of SLI, I just thought it would give you the best preformance for years to come.
Crap, I forgot. The Power Supply, you might need a new one. I don't know how good that Aspire that comes with the case is, but just in case you need a new Power Supply - Enermax Whisper II 535W Dual +12vrail ~$89.