Chosen Solution
I swapped the i5 with i7 7700; Startup population lags but much faster response. diagnostic shows no issue, smc reset did not help. running macOS 10.15.7 I have a Belkin express dock and an Apollo twin X; both worked with the i5 cpu. I also replaced the 5k spinning rust with a crucial 2t ssd and 32g 2400 ram. I tried rebooting back into original drive externally, but there was still no TB.
The PCIe lanes used by Thunderbolt are directly from the CPU. So you either have a bad CPU or the socket contacts are damaged.
