I got back into cycling about this time last year and was shocked at how unfit I was.
Running certainly helped - I did a half marathon this year in a semi respectable time (1:54) and thoroughly enjoyed it and will be doing another one later in the year. I like running because you don't need too much time - an hour after work and I feel like I've done some proper exercise.
What does seem to have made a big difference is buying a road bike - I get out as often as I can mid week now and used it when the trails were too crappy for MTB. I've made a point of getting out of the saddle as much as I can, sprinting up hills etc. I was genuinely surprised how mich better I felt on my first good MTB ride in a while last week.
I lug a silly bike round too - SX Trail, 1x10 gearing, big grippy tyres etc.