Do the vast number of questions asked on the same situation I highly recommend you have a sit down with a local tax pro to discuss all your concerns  and to get educated on the federal & state rules on a1031 exchange. 

https://ttlc.intuit.com/community/user/viewprofilepage/user-id/1325956

I agree with @Critter-3; consult with a local tax professional that is experienced in like kind exchanges.

Further, you can contact a local qualified intermediary for more details on any proposed transaction.

In direct response to your question, some closing costs can be paid with exchange funds while others cannot (e.g., commissions can be paid from exchange funds and would not be considered to be boot). A local QI would be able to provide you with all of this information and more.