I'm curious what if any other companies that are in the situation we are where the work is being performed by the government and a DD-250 is required who is signing? I know of some program work arounds, but decided to ask the question since this seems like it might be something several companies have issues with?
Your contract is managed by DCMA so you will submit your DD 250 to the Contract Management Office for processing. DD 250s may be submitted to the Government either in paper format or electronically.
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As to the question of who signs the DD250. The contract should have identified the government office/individual that signs for the completed work. The Program Office can delegate a government representative to accept the completed work.
If your contract requires source inspection or inspection/acceptance, you will need to notify your assigned Quality Assurance Representative that you are ready for inspection see FAR 52.246-2[i]  and .
I have included DD Form 250 Guidance for the Contractor for more detailed discussion and more references at https://acc.dau.mil/CommunityBrowser.aspx?id=453147.