First of all you've finished cycling if you added fish already... I hope.
You say "cycling for over 3 months...". Not an accurate statement. However, you are experiencing another
cycle not if you've got ammonia and nitrite present. Things may start to die unless you keep up on water changes very often. Make a LOT of SW
and have it ready to go over the next few days.
Flame scallops do not live long from what I've both seen and experienced. The amount of feeding yo'll have to do with keep thet water in a 35g totally messed up. They won't work, believe me. Also, the yellow headed sleeper gobies are notorius for not eating prepared food and starving before long. Good luck with that.
Also, read this about your puffer... http://www.fantasyreef.com/database.php?p=viewitem&dbid=7&itemid=301
Not a good choice for a reef tank. And he'll eat those shrimp before long.
Tell us about your initial cycle prior to adding fish. How did you do it and what were the water readings throughout? Was there rock when you cycled? How much?