Amazon, your local Walmart/Bestbuy will price match if you'd rather buy local.
You could get a 3.0 reader, it would take advantage but if your current one works are you going to really be using it constantly? You can get them pretty cheap though and stay under $30 easy.
Correct, yes you don't need all the tools listed. #00 screwdriver and a good pair of tweezers are also helpful.
The ifixit link was more for the teardown steps rather than the tools needed.
I see them typically $50-100 depending on what's wrong.
Look at ifixit for a 3DS teardown.
Definitely make sure it's completely dry before attempting to turn it back on.
Part it out? Buttons, rubber squares, housing, glass, etc. or even sell on eBay stating what happened and sell as is. I repair 3DS' locally and always on the lookout for components.
As to your second question, anything will work now.
I helped someone using this exact method. All they had was their secureinfo_A and modified secureinfo_A. I used the offset that decrypt9.log showed to XOR the modified secureinfo_A with the nand I pulled with a hardmod and then XOR'ed with the original secureinfo_A.