What you need to do is write that CloneCD Image you have back to a CDR Disc. Open CloneCD & select "Write From Image File" - select / browse to the image & write at say 8x.
Once youve written the image back to the disc - Install the game off that disc, (Select a LARGE Install) then execute (Double Click) the patch youve downloaded to update the game to Ver. 1.0.1.15, (takes a while to update) then replace the original c4.exe with the cracked exe you've downloaded.
In other words you dont need to copy either the patch or crack to the CD. Just create your commanche disc & install the game & run the patch & crack after.
"backupcd" crack should work like a No CD just replace the c4 exe in your game folder with the cracked one.....
From memory when I started the game it still asked me for the CD - but click cancel & you should be right to go !!
Hope that helps.....