I can empathize. I run (and swim) all winter as riding is tricky in the winter around here. I get in pretty good shape running, cruising at 6:45/mile by spring. Getting back on the bike this time of year, my lungs and heart will be barely be working and my quads will just melt on the first few rides. It's frustrating. I'd say it takes me ~12 good, fast 30-40 mile rides to be back in reasonable cycling shape where I can start taking pulls etc. Those first few rides are really strange: I'm not really getting a good workout, but I can barely climb stairs afterwards.
Then again, in early winter when it's time to start running again, that first run SUCKS! For me, the transition back to running is probably harder.