Michael,
Here is an answer I wrote regarding how loan amortization works for most mortgage loans: http://www.mortgagenewsdaily.com/wiki/Understanding_Mortgage_Amortization.asp.
The same principles work in calculating the answer to your problem. From your post it looks like your loan started with a payment due on June 25, 2009 of $311.51. If you make this payment for the next five years you will owe about $27,420 + interest of about $149 on the last payment.
What is confusing is that you are choosing to prepay the loan by paying twice per month or 'semi-monthly.' Presuming that you have the standard terms on your note and you owe 1 payment per month of $311.51/month, paying $250 twice per month is no different than paying $500 once per month. When calculating the amortization of the loan you use a period of 12 payments per year, not 24 payments per year regardless of the amount paid in any one month or when the payment is made. (Unlike simple interest loans.)
It is likely that your Note has interest charged on the loan at the rate of 6.5% per year payable monthly or 0.541667% per month. If this is the case then on the first payment you made you owed $193.65 in interest on a balance of $35,750.00. You made a payment of $311.51. The difference of the payment of $311.51 and the interest due of $193.65 is the amount of your payment that went to reduce your principal balance. ($311.51 - $193.65 = $117.86) So after the 1st payment your balance was reduced to $35,632.14. ($35,750.00 - $117.86) The next payment of $311.51 included interest due of $193.01 ($35,632.14 X 0.541667%). That left $118.50 paid towards the principal, leaving a balance of $35,513.64. ($35,632.14 - $118.50)
On the third payment (due Aug 25?) you paid $500. $250 on 8/1 and $250 on 8/16. The fact that you paid early is of no consequence. On the third payment you owe $192.37 interest. ($35,513.64 X 0.541667%) You paid a total of $500.00. That leaves $307.63 to be applied to your loan balance, leaving a balance of $35,206.01. ($35,513.64 - 307.63 = $35,206.01)
If you continue to pay $500/month the loan would amortize to zero in about 89 more payments. This can be computed by continuing the calculation above until the balance is reduced to zero. If you use a financial calculator to compute this you would put in the balance of $35,206.01 (PV); the interest rate of 6.5%/yr (i/Y); the payment of -$500.00/month (PMT); and "compute" or solve for the term (N). The answer is 88.91 months.
But your loan has a balloon feature. You must pay the remaining balance on the 60th payment + the interest due for that payment. The balance arrived at above of $32,206.01 was after the third payment. So you have 57 months left to pay on the loan. If you continue the manual calculation above just stop when you arrive at the balance after a total of 59 payments. (2 payments at $311.51/mo and 57 at $500/mo and one final balloon payment paying off whatever the remaining balance is).
If you don't want to do that much arithmetic, you can use a financial calculator to calculate the balance owed after the term is up or you can use a spreadsheet. We determined that after the third payment was made that the balance was $35,206.01; the interest rate is 6.5%; you make payments of $500; and the term is 88.91 payments to get to 0. The balance due after 56 payments is about $15,034. There will also be $81.44 interest due. Therefore the last payment would be about $15,115.