Wedding help

For a large order like this I would make the gumpaste / fondant flowers as far in advance as you can. I start as soon as the date is confirmed.

I can't tell you how long they will take to make as everyone works at their own pace, but with a plunger/ cutter it should go pretty quick.

I bake all of my cupcakes on the Thursday & Friday before a Saturday wedding, and mix my buttercream while those are baking.

I store them in airtight bags ( the largest ziploc's made ) overnight.

I then get up at 4 am the day of the event and start piping out the icing and decorating with whatever accent they chose. 

If you have to package these individually I would start the night before.

Cupcakes freeze wonderfully.  I just freeze them and throw them in a ziplock bag or put them in a plastic storage container.  But you will need to do some space calculations to see if you have room in your freezer.  200 is quite a few.  You will also need to plan for how to transport, etc.  You could use short storage tubs to transport.  If you freeze them, you can  place them in the container for transport and ice them right in the tub, add your fondant decor and done.  No need to pick each one up individually, they will thaw while you are adding the decor and while transporting,etc.  Oops, that didn't address the filling thing, haven't done that.  Nor can I help with the fondant decor part.  It really depends on your own personal speed.  When you get the cutter you will just have to make a few and see how long it takes YOU, more important than how long it takes someone else.  Using your recipes you can come up with a list of all the ingredients needed and amounts and use that to figure out your ingredient costs.  Plus liners, etc.

I am a buttercream only gal, can't help you with the fondant questions.