We bought multiple properties and think that we are sophisticated player but it happens to us all the time (especially for attractively priced deals) even though we know the game.  

I like Mint.com for personal use, but would like something similar but more sophisticated for different business entities. 

I am thinking a kind of quality sophisticated smooth jazz instrumental is good.

Issue is the guy managing the properties has no detailed rent payrolls or maintenance but has documentation on the active leases (with deposits) however.  

Have you found that most people understand that terminology, or is there a less sophisticated way you say it to the seller?

You can't elect to be an S-Corp for 2016 but you could for 2018 and beyond.The questions is whether the benefits from filing as an S-corporation are greater than the admin costs that come with it (corporate return, payroll returns, etc.). 

Second question is when payment is made to contractor, we just need to issue them 1099 in the end and have all receipts of payment , do we need to care about payroll tax or any other tax.

And flipping is not investing, it's a project and if you do it well and you can scale it eventually it will be a business with staff on payrole and hopefully a 10% profit at the end of the year before taxes.The only real play in REI is buy and hold - for a long time.

I.E. telephone and advertising costs haven't been accounted for and all the management, payroll, and all types of repairs and improvements are lumped as one sum. 

It probably depends upon the sophistication of your tax team.