FINCHforum

a pic of the type of nest you have given them would be helpful here, but as a rule zebras dont care what size the nest is, they can and do breed in anything. If a bird isnt satisfied with a nest then it tends not to use it, so I would say sit back and relax. hopefully in a few days you will have young birds
always try to supply the largest nest possible for your birds in future though, probably wont faze the birds but will put your mind at ease.

Choxie79, first of all congratulations on the new birds and all the eggs, hope all goes well and you have some babies soon.

Let’s take your Q's 1 at a time:

I have 2 Zebras (it's been only 2 weeks) and they already have 5 eggs. I purchased the basket type nest that were meant for finches at the pet store. I put everything in but by the time I came across an article saying that if the nest is too small the babies can get squished to death, they already had the eggs in there?
Now I am nervous. I think they should hatch in about 8-10 days.
Will they be ok? Should i do anything but wait?

The nest is a bit small but they should be OK, just don't give them too much nesting material so the chicks wont get kicked out of the nest.

Should I separate the chicks by male and female or can they all live together

It is recommended to separate them to avoid fighting and in-breeding (assuming there are nests in the cage), if you have room. If they are still young you should be alright keeping them together though, just watch for aggressive behaviour like feather plucking and so on.

Also whats the minimum on a cage size for 5 birds if they could stay together?

I would say at least 2'x 4' or 5' long.

How long should I wait (if I decide I want to do it again) before they can try the next clutch?

I usually allow my birds 4 weeks rest after you removed the babies so they can rest, but especially zebras might start a new clutch before the other babies have weaned so just keep an eye on them

I am planning on removing that nest and getting a larger one if I decide to let them breed again. Although I read somewhere that if they want to have babies they will find a way (food dish , floor,etc).

They can try and nest in food dishes but if that happens you can always remove the eggs

Should these birds be given as a pair to the next owner or should I try to trade birds to avoid in-breeding? How serious (bad) is in-breeding?

When you sell/give away the birds you must do the responsible thing and mention that they are related. Some bird keepers do in-breed but I believe this weakens the gene pool and should be avoided at all time, its part of being a responsible bird keeper.