Fish:You can move your rocks into the frag tank and/or sump, that will move your biofilter and you won't need to cycle (maybe a mini cycle).
What kind of livestock are you moving?
The corals are all on frag plugs because I knew this move would be happening. But I have a frag rack in the system now to put the corals. I have the light let up over the frag tank and will be transferring the lights from the 40g after.Are the frags mounted to the rocks? If not, here is what I would do, in this order (I do not know if you have enough time to stage this, if not, try to at least get the rocks moved asap with some time before you move everything else):
1. move the rocks to the new system, put them wherever they will fit. That's your biofiler
2. make sure temp and water parameters match between frag/sump and the 40g
3. move the fish
4. move the softies and lps
5. move the sps
The coral is going to have to sit in frag racks or something until you have the new 40g set up.
What are you doing with your lights in this transition? This is "just" a system move, and lots of people move systems successfully, the key is in trying to maintain parameters and also try to keep the stress on the corals to a minimum. The fish will be fine, it's the corals that might be stressed by the move to new flow, light, parameters.
There’s quite a bit My plan was to just start with dry rock in the new system so I never paid much attention to it because it hasn’t bothered any corals.Hmm, bubble algae? Yes, you will be moving it with the rocks. How much is there, can you scrub it off?
I'd be more concerned about getting the biofilter in place, and worry about the bubbles later. If I understand your plan correctly, when you get the new 40g running, you can take care of the bubble problem at that point.
I can set up the 40g whenever Im in no hurry for that (moving is stressful enough lol). Is there a timeline you recommend as far as setting up the 40g/ adding the new rock.Good plan. Keep an eye on your parameters.
In terms of the bubbles, how long do you think it will be before you get the new 40g set up? You don't really have a big bioload, you could start to add the new rock with the old rock in the other tank/sump, and not disturb the bubble algae (that helps it spread) and just start taking the rock out as the new rock gets seeded, keeping an eye on parameters.
Keeping the lights off and using emerald crabs is going to take much longer than just pulling the rock. Using something like Vibrant is another option, but in a system your size, it is just better to pull the rock. Do you plan on reusing the sand as well?
I will mostly likely be using normal dry rock or real reef rock.Swapping the new rock for the old rock is a matter of letting the biofilter establish itself enough on the new rock to handle the bio load after you take out the old rock. In your case, you only have four fish (the coral isn't as much of an issue). What kind of rock will you be adding, and do you think it will be about the same amount as the old rock?
The bacteria will populate everything that the water touches, so your sump, the frag tank, the new sand, etc is all surface area for the bacteria. You could probably do the swap pretty quickly (as in all of it at once), but the best way to tell if you are moving too fast is to watch your ammonia levels.
The risk you take having both new and old rock in the system for a long period of time is that the bubble algae will establish itself on the new rock. It's probably on your frag plugs, so unless you plan to clear all of that (remove frags from plugs, etc), you can be careful with the rock and not add to the risk that the frag plugs already represent.
I hate bubble algae. Most likely you will find that despite taking as much care as possible, it may show up anyway. Key thing is to jump on it right away. And with your stocking list, an emerald crab won't be a bad idea (the ones from reefcleaners.org always seem to work for me).