The account being under the minimum won't cause Fidelity to refuse the account; they are likely to assess a fee if it is under $2500 on the annual date for determining such things, which I think is in November.
You can contribute $2000 annually to an IRA even if you are currently under a retirement plan. It may or may not be deductible if you are under an employer's retirement plan. You can add that $2000 to the SEP IRA if you wish, or you can add enough to bring it up to $2000.
I believe the minimum is $2500 PER FUND so you are for the moment limited to one. You could add just
enough to bring it up to the $2500 total and put the rest in your regular IRA if you wish-- you can have multiple IRAS and can divide up your annual $2000 contribution any way you like.
Best wishes, Chris