Good to see you back, I assume all is doing well!
As you are transferring everything from one tank to another, and using a neutral substrate (gravel) you can probably do it in one go. If you are getting a new filter as it is a larger tank then I would float the sponge from the new filter in the 5L tank for a week or two to get some bacteria on to it, but it looks like you will be transferring your existing filter which can just be transferred as it is. If you are using some sort of active soil substrate you will need to run that in to avoid any ammonia spikes or other build up of nutrients etc before that is put into the new setup, but you say gravel so this is probably not relevant.
I assume you will catch the shrimp and put them somewhere safe whilst you do all the tank work so I would drip acclimate them for a couple of hours to the new water to be safest, once you have completely set up and filled the new tank! If they are neocaridina shrimps you are transferring and the water parameters are very close you would probably be able to miss the drip acclimating, but I would play it safe and drip acclimate though!
You will also need to ensure the water temperature is matched when you go to put the shrimp in the tank as the shrimp may have been in water that has cooled over the time they were put to one side.
How are the tanks doing, and did the small micro crabs work out?
Simon