Hi klexen :
2. Will my backups that I made the old fashioned way with just the "ss.bin" work with the new firmware? If they do, will they have that stealth mode?
Yes your backups will work just fine, and No they wont have the stealth mode.
3. I remember back in the day there were certain sata controllers that would not work, something like ICH6(Just guessing from top of my head) etc.. Well I was lucky enough to have an asus motherboard with sata ports that worked. However, now I have a new motherboard with nforce chipset. "Serial ATA ports supported by nForce3 250Gb chip "
http://www.anandtech.com/mb/showdoc.aspx?i=2198&p=2 <---- Link to my motherboard. I was wondering if MTKflash has a problem reading this chipset,(without hex editting this)
you're lucky enough because I have also an Nforce3 250Gb board,and Yes it works just great with MTKflash without the need to edit anything.
4. If the old way of ripping games works with this FW version, what exactly is this new PFI.bin and DMI.bin for? Can someone give me a quick summary of what these are? Are these the files that make the game "stealth" like I've seen games with "stealth patch"
Yes exactly,these files makes ur backup looks almost identical to your original discs which makes them stealth.
5. Question about 4.1a/4.1b,
4.1a = Quiet/slow 12x speed - Quiet slow readmode
4.1b = Quiet/slow 2-4x - Fast readmode 12x
I'm not sure I understand what the differences are exactly, and which is better for what. Could someone please explain this a little better?
Latest C4E firmwares comes with 2 preset speeds for reading backups,one is Full speed to treat the backup just like an original disc
and this requires U to use good Media for ur backups,the other is Slow speed that will read ur backups slower but much compatible with cheap Media discs.
Each FW have the 2 speeds integrated (Full Speed ~ 12x & Slow ~ 4x) and U need to insert an original Disc to switch the FW speed from Full to Slow
or vice-a-versa,also each FW have 2 versions for example: 4.1a (with Full speed by default) or 4.1b (with Slow speed by default).
N.B: just to let u know that FW from 4.0 and above comes with a special feature that protects the FW from being flashed again Unless U are in the
0800 mode ( which U can turn it on by using the 0800 iso provided with the FW and burned to a Dual Layer disc )
I am still with version 3.2 now and using non-stealth backups because I never use Xbox-Live anyway

I hope u're up-to-date now with FW flashing, and good luck..