Ya know, I was wondering where and how our old friends Mighty Mouse and Underdog would fit in all of this?
How about adding the Mighty Mouse set of characters and the Underdog set of characters to Earth-C. They would each be based out of separate cities, so that their original cartoon adventures could still have taken place.
Mighty Mouse was the first, Golden Age hero on Earth-C; Underdog showed up in the 1960s - his arrivel heralded a new age of heroes; Captain Carrot was added to the mix in the 1980s, the first of the modern "Zoo-Crew" generation.
I'd also like to move Krypto Mouse from Earth-1 (or Earth-B) to Earth-C and give him permanent (or permanently re-occurring) powers: When danger threatens, Fuzzy secretly exposes himself to his hidden piece of radioactive Kryptonite to become Krypto Mouse! There would be a lot of stories playing on the themes of him not turning back to Fuzzy in time, or turning back too soon, or threats of his piece of Kryptonite being discovered or stolen, etc.
The founding members of the JLA (Justice League of Animals) in the 1960s would be Mighty Mouse, Krypto Mouse, and Underdog.
Captain Carrot may or may not have joined the JLA later on, but if he did then he probably had a major falling out with them over some obscure philisophical nit and left to form the Zoo Crew.