Based on my own comeback experience, you're making a number of mistakes.
#1- You're not running every day. Walking, biking, and gym stuff are not running. You need to actually RUN every day in order to progress and develop what you've lost. Running entails getting off the ground with each stride.
Jogging barefoot for 10' on the treadmill each day would be much better compared to what you've been doing. Daily bouncing from one foot to the other while swinging the opposite leg forward 100 times in a doorway can be helpful for a warmup (my version of the 100 ups exercise).
#2- Doing a time trial on a trail was asking for trouble, and you got it. You need to have a flat smooth surface for a time trial, either a track or else a similar smooth flat level surface.
#3- Running uses your calves completely differently than cycling, which is exactly why they started hurting. You'll be lucky if you didn't already get injured. You need to take it easy at the start and gradually build up the running movements and tissues.
#4- As you get used to getting off the ground and your calves get used to the exercise, you could start doing some moderate 100m repeats or the equivalent, not for speed, but simply to get used to getting off the ground, which is strengthening for your unused muscles, tendons and ligaments. Also it's a step up in getting your calves and rest of your legs used to the exercise.
#5- Walking can help your progress, but it's not a substitute for the necessity to keep doing some running each day and progressing. Cycling and gym work won't help your running at all and are more likely to be counter productive.