So after a battle when you can upgrade and purchase ships can you take a ship out of your fleet? For example if I have 2 MC80s and a CR 90. Can I pull the CR 90 out of my fleet to purchase more upgrades or squadrons?

No, once you take ships and upgrades, you test up your receipts. You will be able to move your non-title upgrades, but what you got, you got.

Not only can you move your Non-Title upgrades, you can even take them off and leave them off, effectively "Storing" them in a warehouse.

But you keep them. You're not able to sell them for points back or anything...

And the Rules are silent on ships, so assume when you purchase a ship, you have it until it explodes messily.

That makes building the Fleets at the start of the campaign very interesting

Yes, it seems like part of the campaign is not just growing your fleet, but finding a way to efficiently "evolve" it from a one-upgrade-per-ship form into a more powerful version that uses the same basic ingredients. Players who can find a way to shuffle early upgrades around rather than replacing them will have an edge.