Dual Boot Windows 7 + Linux on 2 separate SSD + Data HDD
Not in order, and not covering everything you need.
Do you want the boot partition for windows? this is primarily for disaster recovery - and needs about 200 mb. In any case, its probably simpler to install windows first and linux second, especially if you want a single bootloader to select between OSes
does your bios let you select between boot drives?
If so, you can have independent boot loaders - you can choose where to install the bootloader while installing linux, and unplugging the windows drive while installing linux is not a bad idea
Otherwise, install windows first, install linux, telling it to install grub to the windows drive. If you want to use the windows boot manager as the primary boot manager, you can set this up with easybcd
Unplugging shouldn't be necessary except to avoid user error when installing boot-related things,
swap partition Well, depends on your usage patterns. Swap has two purposes on linux - for hibernation (in which case, you'll want one at least as but as your ram. Chances are you won't be using swap much with 16 gigs of ram, so setting it up on the data drive isn't a bad idea.
AHCI - with a windows 7/linux combo you shouldn't need any emulation to install anything
Partition sizes - modern thinking seems to be one big partition for everything.
for the drive sizes and oses your using, partition alignment shouldn't be an issue. Its mainly an issue with XP or older and AF drives.