I believe leftover points can be used for anything also read the flex points for each module some are restricted (you can spend these points on ...) other times they are unrestricted.
as far as the other issues
atow is the rpg rules book it is basically an adsvanced game book for the roleplaying it has the rules to create and run "people" in the battletech universe
total warfare is the mech vehicle combat and tournament rulebook
tech manual is the vehicle construction rulebook
tactical operations is mostly the planetary combat rulebook
strategic operations is the system, and interstellar rules
the various tro's are books of combat units, typically any TRO from a date earlier than a given year can be used, IE you want to play in 3035 you definately could use anythign from 3025, you MAY be able to use things from 2750 (but they need to be justified) and 3039 you can use many things (flavor text or mul {master Unit List} should be checked) 3050 is mostly going to be unavailable, wheras if you are playing in 3075 well that changes the available units significantly.
as far as determining unit costs you would either need tech manual, a unit price list, or something like the mercs handbooks, or some resource that lists the actual costs.
the best news for a battletech campaign is that honestly most of the time specific prices may not matter, as plot issues may override.
additionally software such as heavy metal does have prices for most of the mechs or other units in the application, and it will calculate the prices for you on any custom units you shoose to create.