1. Choose the regular install. However by default that will use VGA/keyboard for its console so….
2. Install to the HD on a different machine, one that has a CD drive, keyboard and monitor!, and configure one interface. Boot into pfSense and enable the serial console. Move the HD back to the Alix (I confess I'm not familiar with any quirks the the ALix might have regarding HD booting) and boot, it will fail at the mountroot> prompt. Point it at the correct path for root then edit the fstab once booted.
3. You can but why do you want to? You're going to want DMA if you're using the drive as a squid cache.
4. Some machines have an issue booting from large partitions but most don't. Stick with the standard partition scheme unless you have good reason to change.
I've never tried that on an Alix so maybe there's some some workarounds to be done that I don't know about. ;)
Steve