I am using the transcript Copy from the IRS website is there going to be any issue if i do not use the EIN number since some of it is blanked out?

For a W-2?  Yes, you need the enter 9 digit EIN to enter on the W-2.  If you do not have that information then contact the employer.

Are you talking about a W-2 that you don't have but are getting info from the transcript about?

You won't be able to efile your return without the EIN. You would have to print and mail your return. You should request an extension to file if you owe and pay the estimated taxes owed. Then you can get a copy of your W-2 from your employer and file a return that includes the EIN. 

If you are getting a refund, there is no deadline for filing your return so you don't even need an extension to file later.