did you actually have a Y class ticket or do you use the term Y to indicate coach; Y class is a full fare coach and for roundtrip transcontinental that could spell over 3,000.
When you say F class is that a full fare First class or you are using F as a term for First class?
Do you have any elite status with CO?
There are several ways of upgrading with money to first class;
you can buy up to a higher fare in coach and then get upgraded.
You can actually buy directly into a first class fare.
The amount of miles you get in each case many vary.
But I think that if you actually buy into a first class fare (any first class fare) and you pay with money (not miles/co-pay) then you should definitely get the miles that come with the first class fare.
If you kept good documentation of the entire purchase process and boarding passes, I would mail it in to CO onepass.