Ok as for your system not wanting to boot up when you have changed the Master and slave position, its really strange ! as it should not have anything to do with the system booting up as your HDD is in a separtae IDE channel.
If I had to guess, I would say that it probably have something to do with your bios settings, if you can have a look at the bootup sequence and confirm it again, just to be sure.
As for not being able to change the Transfer mode in the Bios, still I had to guess, I would say since the Bios does not detect the ATA66/100 cables it would remain defiant to allow you to change the transfer Mode.
The Damn PIO mode or any of its many varierties are painfully Sloooow !
As for the IDE ATA66/100 cables you are spot on, make sure that they are a decent quality as they are a lot of imitations are out there.
The tip end of the 40pin or an 80 Pin cable are exactly the same and are universally standard and would fit the same way as the Normal 40 Pin IDE cable would fit in.
The only difference between these cables and the reason they are called 80 as oppose to 40 is the number of little tiny wires that make the ribbon IDE cable are doubled in the 80 Pin cable, thus reducing resistance to the information flow.
Now as for your chipset, first identify exactly what chipset you have by the identification utility that is listed on the same page Identify your IntelÂ® chipset and next try to update your chipset using IntelÂ® Chipset Software Installation Utility.
At this stage with your new IDE cables in place, try to do a test run on your burner doing a simulation to see any speed difference.
If the difference is still not quite there, then try the Next utility on the Intel page which is called IntelÂ® Bus Master IDE driver and then repeat the same test and see if that has made a difference.
I would not worry about IntelÂ® Application Accelerator, as it really does not do much here and is better left off.
Finally have a look at this URL to give you a better understanding of all of these IDE transfer mode jargins,
Its a bit of reading but it would make it a bit easer for you to get a good over all picture.
While you are at it make sure to grab the latest Version of Clone which is the Clone CD V 188.8.131.52.
You can read all the details about it and what it does in the main forum and Clone Forum.