This response is based on the information provided.  We suggest you discuss with your contracting team, program manager and/or legal department as appropriate. 

The contractor is required to perform within the terms of the contract, i.e., FAR 52.216-16 for this issue.  Per FAR 16.403-2(c)(1),  "The contractor’s accounting system is adequate for providing data for negotiating firm targets and a realistic profit adjustment formula, as well as later negotiation of final costs."  If the accounting system is adequate, the contractor should be able to segregate costs by CLIN/subCLIN.  We would think that work falling under FPI vs. cost plus fixed-fee, vs. firm fixed-price CLINs would be different work packages.  The contractor is going to have to show costs related to FPI and cost plus fixed-fee discretely (with FFP separated out) to reach final price settlement.  It should be doing that now.

If FFP and FPI work is being lumped together and you cannot get the contractor to segregate, you can look at the total value of the CLINS and subtract the FFP CLIN values to see where the contractors costs are.  You can also look at spend patterns from previous reports to project future progress.  If the contractor disagrees, it has to support its beliefs with numbers, data.

As for DCMA training, we agree it would be nice if the contractor provides ETC data.  However the contractor is again is bound by the terms of the contract.