| Non-expert thoughts. I think a calorie counter on a machine is a decent gauge... for that machine (it's just based on weight, speed, & difficulty [incline]). Machines will vary between eachother. I can totally see 3.5 at a "12" incline being the same as 5.2 jogging at "0" incline.
You're working muscles differently with the walking & running. Your instinct about backing off speed is correct. If you can't truly do an exercise at a certain speed then you need to chill. Can you do 3.5 at 0 incline? Yes? Then scale the incline up to the level where you can't do it for the whole workout and back off. It's OK to have a workout that is "easy" and then bump up the intensity next workout and keep gauging. | 
