Converted from 30gal to 55gal Help!!!!!

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You can try to get them out using a fish net, a fine strainer/sifter, a slotted spoon, etc. As long as your fish don't eat them, then you should be alright.
 
ammonia hides in the gravel where it is most concentrated. If you can siphon the water from around the gravel, without (like you said) disturbing it too much, it will decrease the ammonia ALOT faster, without damaging the cycle.
 
Just giving everyone an update, my tank is cycling. The ammonia is down to 0 and now my nitrite is going up, so my tank is going through a mini cycle. Thanks for everyones insight.
 
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