What if my employers EIN is too long? It's 11 characters long instead of 9 but that's what they have on file. Turbo tax won't let me enter the 11 character one

Did you ask your employer?    An EIN is only 9 digits xx-xxxxxxx.   Does it have any leading zeros on it?  Is this on your W2?  Even a  social security number is only 9 digits.  

All federal EIN numbers are 9 digits.  It should be in Box b of your W-2.    It can be different from a state ID found in Box 15.

Anything that is 11 characters is not an EIN. Ask your employer what their correct 9-digit federal EIN is. (The hyphen doesn't count. The format of a 9-digit EIN is nn-nnnnnnn.)

What do you mean by "what they have on file"? You should be getting the EIN from box b on your W-2. If it's more than 9 digits, the employer did not fill out the W-2 correctly.