Is L1 to H1 transfer with COS counted against the annual cap of 65,000 ?

Yes, assuming the H-1B petitioning employer isn't cap-exempt. All except cap-exempt _initial_ H-1Bs are counted against the cap, initial meaning first H-1Bs or first H-1Bs after a person previously on H-1B has spent at least a year abroad. L-1 time is counted with your H-1B time towards your six permitted years in H-1B status - but it doesn't get you out of needing a cap-subject H-1B.

Yes, unless the H-1B position is cap exempt.

Yes, unless cap exempt. Goodluck.

Yes, unless you had the H-1B status in the previous 6 years or it is cap exempt.

Yes, this will be counted against the cap. Also, the years you spent in L-1 status in the U.S. will count toward the 6-year maximum period of H-1B eligibility.