No you probably shouldn't have your deposit be your entire down payment, in every market I've done the normal deposit is somewhere between 1% and maybe $10k-$15k max so unless you are doing FHA with a really low down payment it probably wouldn't make sense to have them add up to the down payment.

Showing a occupied unit works for some but even on normal circumstances I wait to show until it is vacant. 

A normal year sees both supply and demand begin to rise sharply in early January, and then reach a peak in late May.

Sounds like you've had your home inspection, and will get the normal warranty deed with title..

Are total closing cost amount normal for my type of loan?

Usually collecting a fee is how if is normally approached.

If you close in 45 days with a normal owner-occupied loans, you should be able to make competitive bids. 

Let him go month to month, you can do the normal rent increase. 

Is it a normal practice?

Has it become normal in this market for the buyer to pay the difference in the appraisal and the offer(3k-10k) in which in some cases basically pays the sellers closing cost?