If you booked a cash ticket in WT+ and then upgraded to CW using Avios, you only earn Avios and TPs for WT+. The same applies if you received an op-up (which is what I infer from your use of "free upgrade").

So the numbers look correct for your JFK-LHR flight: 100% of flown miles on a T class fare, plus the 100% Gold bonus.

Incidentally, although you've already flown the itinerary, you might still want to think about editing out the booking references from your original post.