Hey now, don't forget the Germanic pagan roots - Lent is during a time of year when all the food stores have run out, and there will be limited rations until the ducks migrate in and provide meat and eggs (Easter).
Also, there is value in many of the things you mentioned. Abstinence from unhealthy things that feel good, engagement in healthy activities that feel terrible, and a general ethos of self control are great defenses against akrasia. Also, hygiene is important, and intermittent fasting may have some benefits.
As I understand it, Lent is a holiday where we celebrate the scientific method by changing exactly one variable in our lives for 40 days. This seems like a convenient Schelling point for rationalists to adopt, so:
What variable are you going to change for the next 40 days?
(I am really annoyed I didn't think of this yesterday.)