Is the word order flexible in indicative sentences (not questions)? Does 'Velký nejsi' and 'Nejsi velký' mean exactly the same?
Yes, it is fairly flexible. In this case the two are identical.
Would this be "velká nejsi" when spoken to a woman?
Why not "You are not tall"? I didn't report this answer, but maybe I did wrong...
I think it is possible, because we often say velký vhen we mean that the person is tall "vysoký". I recall adding it elsewhere before so I will also add it here.
If I added "ty" to this sentence would it be correct to say "ty nejsi velký"?
Is there punctuation to indicate a question? ...or is the order of the words the indicator?
It is a declarative order. The punctuatuon determines if it is a question (?) or not (.).
So there's a separate verb for "not to be"
no, this happens to be the common verb negation by prepending "ne".