Unable to boot as drive is inaccessable

Welcome to sevenforums. :)

Can you post a screenshot of your Disk Manager? I have a sneaking suspicion that the system reserved partition is still on the 3TB drive. That small hidden partition is necessary to boot windows 7. It's easy to fix, but I want some proofs before I send you doing stuff.

Write "disk manager" in the Start searchbox to find it quickly. Here tells how to post a screenshot.

Ok, so it is just an issue of Active partitions.

If you see, both the HDDs are marked as Active, when only the boot partition (C: in your case since you don't have that system reserved partition) should be marked as such. And yours isn't.

It's a bit more complex than anticipated.

From Disk Manager rightclick on C: partition and select "mark as active".

Open command prompt with administrative privileges, (this tutorial), then write
diskpart and press enter
list disk and press enter
select disk 1 (which is the 3 TB hard drive, you can see its number in Disk Manager) and press enter
list partition and press enter (t should list only one partition called Partition 1, the size as you see in disk manager)
select partition 1 and press enter
inactive and press enter.
now we do the same to the 1.5 TB disk
select disk 2 (which is the 1.5 TB hard drive) and press enter
list partition and press enter (t should list only one partition called Partition 1)
select partition 1 and press enter
inactive and press enter.

You should now see from Disk Manager that either of the two hard drives is no more marked as Active.

Then you reboot.
If it still fails booting this time (which would mean it is missing boot files as I was speculating above) you need to do a startup repair, this tutorial, and you should be good to go.

Btw, is there a reason to have more than 1 TB of unallocated space on your 3 TB hard drive? (so that in My Computer you see it as a 2 TB drive, not a 3 TB drive)

What does making them inactive do?

Tells the BIOS that they don't contain boot files. The BIOS (the motherboard's firmware) does not have the smarts to find out this detail on its own.
So it won't try to boot from them and then giving errors like this guy here did experience.

Your issue was caused by C not being set as Active, but marking the other drives as inactive will avoid other issues in the future. They are data disks, not system disks, only system partition (or the system reserved partition if you have it) should be marked as active.

It's sized to 2TB due to the MBR formatting

I assume you did it to be able to boot it, as maybe your motherboard isn't able to boot a GPT disk. Anyway now that it is back to being a data disk, you can get it back to GPT by following this tutorial.

I hope your C drive has been marked as active as well, as I said above.

That System in the wrong place may need you to do a startup repair up to three times as in this tutorial, in case when you reboot without D it fails to boot again. (do startup repair without D connected)
As that drive seems to still contain boot files or components of them anyway, and a startup repair is the fastest way to fix the issue.

Then after you got the SSD working fine on its own, you can connect the D drive again, reformat and rebuild the MBR to erase any possible trace that it was a system disk (to not confuse the BIOS). Moving that disk to GPT as in the tutorial above should do the trick without more command prompt magics.

The problem seems to be simple. Your Disk0 (SSD) has no bootmgr. It is sitting either on Disk1 or Disk2. Leave those active and copy the bootmgr to C:

Bootmgr - Move to C:\ with EasyBCD

The set Disk0 as first boot device in the BIOS.