Refer your client to the instructions for the 990 for an estimate, if you don't know https://www.irs.gov/instructions/i990#idm140359632083680

I have attached their average time estimates for reference, so just tell them 85 uninterrupted hours should do the job. 

Just tell them it takes less time if they (a) have a complete set of books and (b) quit bugging you.