Mortgage underwriter issued a conditional approval- questions

I am in process of closing on a home. I am pre-approved for a VA loan with 0% down. My estimated cash to close at the moment is $6400. I have already paid a $1000 earnest deposit and paid for the appraisal. I have $3000 in my savings account. I will have the remaining $3400 in the next few weeks from my paychecks and also a $1500 ‘gift’ from my boyfriend. He will be living with me but will not be on the loan. The underwriter just issued a conditional approval, and one of the things requested is an explanation of why I don’t have $6400 in my account at this time. Do I just explain that I am still saving? Is that going to mess things up? Can we still proceed or will they want to wait until I have the full $6400 to move on? Also, since my earnest deposit is $1000, will they require the full $6400 or just $5400?The closing date is July 20th.

I want to add that I make plenty of income for the mortgage payments, I just did not save in advance as it was a bit of a last minute decision to buy instead of renting another apartment. I was fortunate to have my very first offer accepted. I did not anticipate it to actually move this fast.