As a Financial Management SME, I can only answer the issue on the RDT&E funding that crosses fiscal years.  As per the Financial Management Regulation (FMR) 7000.14-R Volume 2A Chapter 1 Paragraph 010214, you can ask for permission from the Comptroller to fund in the first year a contracted effort that is greater than 12 months but less than 18 months if one of the following is true:  a) the effort is not logically divisible; b) it is infeasible to shorten the contract length; or c) you do not expect bids if the contracted effort is not fully funded. 

I would also expect to look at the Budget Exhibits to determine what you included for this particular effort.  The RDT&E funds have to be in the Current phase, so available for new obligations (if this is a new effort).

I strongly suggest you seek guidance from your Comptroller, and/or Legal office for this particular issue.