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I sealed and filled my guitar using ca, did it three times and all looked well and smooth and i could see the ca in the pores, however when i sealed again and put on three coats of the finish(em6000) it looked as if a majority of the pores hadnt been filled at all what should my next step be? Should i sand down the back and sides and refill or can i fill over the three coats?

What viscosity of CA did you use? If it was level after it cured and you sanded it back to wood, it should be level.

I would spray some more coats of the finish. It does shrink back and it will find any voids at all. If it were me, I'd shoot another 9 coats and let it cure for a week. Than level sand.

It is also hard to give this advise though without seeing the guitar body. Can you post a picture at all?

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Well I CA fill mostly these days. I use medium thick viscosity from StarBond. it has a good open time. On very open pore woods like IRW it takes 2 and sometimes 3 sessions to fill but most of the time just two. on med-light pore woods one is all it takes. I never seal the wood before I pore fill. I pore fill scrape or sand flush then seal i want the CA to bond with the wood not a sealer. Now I am of course speaking of hardwoods not softwoods like Spruce and Cedar and never where end grain infiltration is probable. I would be concered with possible reaction and or adheision issues sealing prior to applying CA