I had the same issues a few years ago switching my groups campaign over to Alpha Strike, but couldn't find a good official long-term campaign system for AS... Luckily there was a gentleman on the Battletech International FB group who wrote up a very well done fan-made Alpha Strike campaign system using a modified Warchest system. It deals with a simple but common sense system for unit reputation, getting contracts, downtime upkeep, and lots of other details, by converting WP (warchest points) and PV (Alpha Strike Points Value) into interchangeable SP (Supply Points). I think he made it using pieces from older Btech merc rulebooks and campaign systems, and we we love using it. It works really well.
Its available on Scribd still under "Battletech Alpha Strike Campaign Rules" by Randal Snyder. Or if you are in that FB group, it's still in the Files section I believe.