I don't overthink the accuracy of my step count—and setting your stride length will only affect the accuracy of your distance.

All that matters is the accuracy of your Fitbit burn. I lost the weight and have maintained for ten months, so by definition my Fitbit burn is TDEE. Trust your Fitbit for several weeks, then reevaluate your progress.

While editorgrrl is right about not over-thinking the accuracy of your step count, it would bug me if it missed 40% of them, even if the calorie burn it came up with were accurate. Plus, I doubt that it would be accurate with that big a shortfall. So, it may be worth some trouble shooting - and even contacting Fitbit customer support.

Have you truly tested it? When I'm just moving around the house, I do think it misses some steps. However, if test it with a sustained walk - say 100 or 200 steps - and count my steps carefully (usually by counting every time my right foot hits the ground and then doubling it) it is generally exactly right.

Some things that I have found can cause missed steps are holding onto a shopping cart (or stroller, etc.) and light or irregular steps (such as when I'm moving around the kitchen, cooking). I don't worry about the latter case. As editorgrrl recommended, I don't over-think the accuracy of my step count.

For shopping carts, it depends on the nature of the trip. If I'm just doing a relatively short trip to the grocery store then I try to not hold onto the cart with my Fitbit hand as much as possible, but don't worry about it beyond that. If I'm doing a major shopping trip to Costco, then I turn off the HR function and put it in my pocket (in my experience my Charge HR gives bizarre, and exceedingly elevated, readings if I don't turn off the HR function before putting it in my pocket).