Is there a GOTS or COTS software package, preferably already in use in the DoD and certified for use on DoD networks, that will present data showing an optimized spend curve that takes color of money and appropriation year into account?
Unfortunately the short answer to your question is no: there is not an automated GOTS/COTS tool that will prioritize funding distributions to individual CLINS/SLINS.
There are however a few existing tools that will assist with building of your automated system:
1) OUSDC Rule-of-Thumb Acquisition Obligation and Expenditure Rates - single-sheet reference is to provide the Obligation and Expenditure Rates utilized in assessing the execution performance of the MILCON, O&M, Procurement and RDT&E appropriations. https://www.dau.edu/tools/t/OUSDC-Rule-of-Thumb
2) Funds Management Platinum Card - convenient quick reference to key DoD funds management definitions, policy, and processes. It includes the appropriation life cycle for current, expired and canceled funds. https://www.dau.edu/tools/t/Funds-Management-Platinum-Card