Complicated Migration - Need Advice

Hi, I have a somewhat unusual situation for a migration I want to do. I want to migrate my Windows 7 install from the current C:\ to a new SSD I have arriving, but there's a few hiccups that prevent me from being able to follow the normal advice.

C:\'s physical drive is currently a SATA-2 (3.0 GB/s) old school platter HDD plugged into a SATA-2 (3.0 GB/s) port on my MB. The physical drive is also home to GNU Grub instead of the usual Windows boot loader and an Ubuntu partition I haven't used in years and do not want to copy over to the new SSD. Tired of wasting 150 GB over something I never bother with.

I have Acronis Disk Director 12 and True Image 2015, though frustratingly I'm not finding my key for it (but my new SSD might come with another key anyway).

I want to copy/clone the C:\ partition from Disk 0 to the new SSD, doing whatever is necessary to make it bootable. Then once it's ready shut down, remove all other harddrives except the new SSD. Boot up into it, do whatever else is necessary to get Windows happily booting off the new drive, then re-introduce the other drives.

Like I indicated earlier, the current drive is connected to a SATA-2 (3.0 GB/s) port. Obviously, I don't want to connect my SSD to a SATA-2 (3.0 GB/s) port and intend to use one of the SATA-3 (6.0 GB/s) ports, but they're on a separate controller on the MB and as best I can tell are numbered as 5 and 6. I know conventional wisdom for a migration is to always plug the drive into the same SATA port, but that's really not an option for me. So can this even work? And if so, will it be undone when I re-introduce the other drives, because I don't want to wipe the current HDD just yet (I want to give the SSD 30 or so days to make sure it works fine before I wipe it)?

So my questions:
1) I know I need to copy the C: partition to the new SSD, obviously. Should I also copy the 100 MB System Reserved partition? Remember, I have a Ubuntu partition and GNU Grub that I really don't want copied.
2) I'm 95% sure I do NOT want to copy the NT signatures when I copy the drive, since both disks will be in the system in the end. Will this cause any issues with making the SSD use my current install?
3) Will it be okay that I'm not using the same SATA ports on my board for the new SSD? Is there any way to make this okay if it's conventionally problematic? I plan to set the boot priority in BIOS when I re-introduce the other drives, of course.
4) Will there be a problem with re-introducing the old drive now, or should I be waiting until I'm comfortable with wiping it? I'd really rather re-introduce it once I have the new SSD booting.
5) Any advice over which to use (Acronis Disk Director 12 vs True Image 2015)? Suggestions on settings/tools/operations to use would be appreciated!

Thank you for the help. It's annoying when 100% of guides assume there's no problems with copying the entire physical drive and re-using the same SATA port, leaving those of us who don't fall under these use cases very unsure of how to proceed.