What I did to transfer the data from the CD-based system to a CF card required to go through a few hoops, but in the end, all runs well.
On a normal day, the 6000 system boots from the ROM on the IO board, and it contains all of the necessary boot routines to initialize the IO board as well.
To capture that ROM data, I attached a floppy drive and copied all of the files from C:\ to the A:\ .. I had to manually make a directory called "CDSTUF" on my floppy, and transfer the file from C:\CDSTUF to that directory.
Next, I took the floppy over to another PC that had running Windows 95 on it, but in DOS mode (when booting Shift-F5 just to drop into command line). I ran "SYS A:" to make the floppy bootable. This will replace the ROMDOS stuff, which is fine. I also copied FORMAT.COM SYS.COM and FDISK.EXE to the floppy from C:\WINDOWS\COMMAND (if using DOS, these files are in C:\DOS).
On your XL IO board, remove the jumper for JP1. This will disable the boot ROM on the system, and will force it to either boot from floppy or hard drive.
On the XL, remove the disc from the CD-ROM drive, and then disconnect the CD-ROM from the motherboard. Attach the CF card, and attach the power via the small power supply cable. In my experience, the CF card cannot be powered from the motherboard, and will cause the system not POST at all.
Go into the BIOS, and perform the IDE Hard Drive auto detection process so it can populate the drive. Also change the boot order to A: and then C:.
Boot from the floppy, but press F5 so it does not load all of the Megatouch applications and drops to a plain command line.
Load FDISK so partitions can be configured. If there are any existing, delete them so the drive is completely empty. If this is the case, you may need to reboot, then re-enter into FDISK to begin creating partitions.
Once in FDISK to then create partitions, the trick with the CD-based systems is to have your Megatouch data appear on drive F:. This will require creating one Primary partition, this can be small, say 30mb, and is used for the boot data. You will need to then create a Logical partition (this is like a bucket that can hold the Extended partitions, make this big, say 800mb!), which then can hold the remainder 3 partitions. When creating the first "Extended" partition, this can be small, say 30mb (this will fall as drive D:), same for the second "Extended" (Drive E:). The 3rd Extended will need to be at least 700mb to fit the CD data (Drive F:).
Once done curating the partition settings, in the main menu of FDISK, set the 1st Primary partition as the Active partition. Exit FDISK and reboot the system, and boot again from the floppy, and drop to a command prompt (Shift-F5).
Once at the command prompt, type: FDISK /MBR (This will make sure that the master boot record data is written to the CF card so it can boot. I had to do this on mine, otherwise it wont).
Next, you will need to format drive C: and F:. Perform: FORMAT C: /S This will format the C: drive and make the CF Card bootable. Once this completes, perform: FORMAT F:
Formatting drive D: and E: are optional, you wont need to use them, they are placeholders.
Once the formatting is complete, you can copy the data from the A: to the C: .. remember to create and copy the data from the CDSTUF directory as well.
Next, attach your CF card to a computer where you can place the Megatouch CD at the same time. Copy all of the data from the CD to the 800mb partition on the CF card.
On the XL machine, re-enter the BIOS and change the boot order from A:, C: to C:, A: for a faster boot process. You may also detach the floppy drive.
Boot the XL from the CF, and all should be well to start into the Megatouch application.
System starts and loads everything a ton quicker. From power on to game selection menu, it takes 45 seconds.
I hope this helps anyone moving away from CD's to a CF card..