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Unfortunately these additional warranties for used vehicles are generally not very valuable for consumers. They have many different exclusions that eliminate coverage for most needed or expected repairs.
However, with that general understanding, that does not mean you should simply accept the denial from the carrier for the two repairs you have had done.
Read and review the insurance policy that you purchased carefully. The insurance company should have provided you with specific clauses or terms that supported their denial of coverage. See if you can find those clauses, and see if they really support the denial or not (they may or they may not).
If your review of the policy shows that the repairs should have been recovered, file an appeal of the denials to the insurance carrier. (They will have a formal process to go through, and even though you may be beyond the formal deadline for filing one, get one in anyway, and request (demand) that they provide you with a formal basis for their rejection if they deny you a second time).
Assuming you have found that your repairs should have been covered (I am guessing that your transmission at least should have been covered, the brakes may not be), and the carrier refuses to change its position, you can then file a complaint with the VA Dept. of Insurance: https://www.scc.virginia.gov/boi/complaint.aspx.
If that fails, you can sue the insurance carrier for "bad faith" (this is simply a special type of breach of contract lawsuit).