Late to the party but I also have a Gateway 2000 4DX2-66. These systems will not work with CF cards over 2GB usually. Although the BIOS may see a 4.1GB HD I have yet to get it to recognize it. I have had some success with using IBM Desktar drives 10-15GB. They usually have a jumper to limit it to 2GB and I have found these to work in older systems.
For me I have had the best success with the the cheap Amazon IDE to CF adapter that has a built-in slot cover. You install it in an unused slot and the CF card is out the back. (The slot bracket can also be removed and the adapter installed on a 3d printed bracket) Not ideal for these mini AT desktops but since I only use a Network card and a Soundcard in this particular machine, it works for me. I do have a Gateway 2000 P5-100 full tower and also use it in that. Same thing though, more card slots and more drive bays, but with a NIC, Video Card, and a Sound Card I don't really use the other slots.
For CF cards, I have only had success with Verbatim 2GB (Tried 4GB and it is not recognized) and Transcend 2GB or lower. 2GB is perfect for my use since DOS 6.22 primary partition is max 2GB.
Anyway, in case you need it here are links to the parts I use (not affiliated links)
CF Card adapter with PCI bracket (Amazon) (When you get the adapter clean the solder contacts on the board as they leave residue behind)
Transcend 2GB CF Card (Amazon) (You may have to click
buying options as these frequently go out of stock)
Also we are trying to get together Gateway 2000 documentation and there is a thread for this here:
One question I have on this is why the drives on these old machines cant be read by new machines via an IDE to USB Adapter? Any tools that I can use to clone over older formatted drives to another drive easily without trying to go the laplink type route?
As stated already, the USB adapters do not work for these old drives. I keep around an old Pentium III (800E with Voodoo5) and an old XP Lenovo Think Centre for these very occasions. They have onboard IDE that can work with these old regular IDE drives. I can usually make a backup from there. I also just install one of the CF card adapters as a slave drive to the system and use XCopy and MS Backup to backup the contents. I did this recently on my 4DX2-66 as it has the original 800MB drive with original install of DOS 6.22 and WFW 3.11.