Hello
First off this sounds complicated and you definitely need to see someone. This wont get better with advice from the internet. I am not a chiropractor but knowing what they do and the position you describe, sounds like he did 'the dog' on you and tried to manipulate your spine, however I may be wrong.
One thing that stood out for me was the bike accident. Your lack of neck range of motion will definitely be affecting your thoracic spine, particularly as you are active (a good thing) so where the neck movement stops, another structure will have to take over. This is made even worse by the fact you have a problem with the lumbar vertebrae too from the MRI which puts even more stress on the thoracic spine. What is your shoulder range of motion like? Can you lift your arms above your head?
Also what are your easing factors?
I would go light for the next few weeks on the weights and forget about sit ups. and also, cycling is not great for the thoracic spine, or any of the spine for that matter. This doesn't mean you have to stop, but if you are cycling, make sure in the gym you are doing exercises to balance it out.
I think the problem is due to poor range of motion in other parts of the body which has now affected the thoracic spine and lack of treatment.
Hope this helps,
Ben