In 2004 I was convicted of larceny and was ordered to pay restitution within 2yrs.I paid a third of it but couldn't pay it all within the 2yrs.I still received the charge of larceny can I now get my money back?Why are they able to keep the money I paid to keep this charge away yet I still got the charge?I am now applying for a provisional pardon but can I go back to my local courthouse and ask for the charges to be removed?I have not been in trouble since or before then.

... Why are they able to keep the money I paid to keep this charge away yet I still got the charge? ...

Because "they", the victims, were not being paid to allow you to "keep this charge away". They were being paid to compensate them for whatever harm you did to them.

Also, because you didn't comply with your part of the deal.