Generally, speaking, accountants will qualify for the "learned professional" exemption from overtime. This exemption allows the employer to pay a flat rate salary without regard to the number of hours actually worked with no overtime.
However, in order for the exemption to apply, the employer must always pay the same flat rate salary--they cannot make adjustments based on the number of hours worked in a day or otherwise treat a salaried employee as if they were hourly. The fact you were asked to subtract hours for lunch would allow you to argue that your employer forfeited the exemption, thus entitling you to overtime.
Regarding your second question, no law requires employers to offer vacation and so the law affords employers a lot of discretion with regard to how and when it can be earned, used, and paid upon separation of employment. In general, employers are only required to pay accrued vacation if there is an agreement so providing. Here, you indicate that you would not lose your vacation. So, you would be able to argue that you have an agreement requiring the payment of your vacation and you could pursue compensation for such hours on a breach of contract theory.
Both of these claims can be pursued by filing a wage claim with the CO Dept. of Labor here. However, if the amount you are seeking exceeds $7,500, you will need to file a lawsuit in civil court, as the Dept. of Labor cannot recover more than that amount for you. To pursue a lawsuit, you will need an employment attorney. You can locate such an attorney here. Most will be willing to assist you on a contingency fee basis, meaning you pay nothing up front, just a percentage of whatever your recover (typically 1/3).