It would probably be best to go with a Mini and an LCD imo.
The eMac board is pretty big if I recall (including all needed attached boards and heatsinks). The G4 iMac might fit but you *might* need a new LCD.
You will also want to watch out for crumbling iMac plastic, the grey stuff is the worst as it is most brittle.
You do know that doing this will most likely involve ditching the iMac's stock CRT right? There just is not that much room in the G3 iMac, unless you squashed a Mini in there somehow. Don't hold me to that though as I cannot remember how much room exactly is available under the EMI shield.