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.)
I am not interested in adopting steel-manned Christianity one tradition at a time, though it does provide many convenient rationalist Schelling points. If I need rationalist communion, confession, abstinence, washing of feet, blessing of throats, or Paschal celebration, I will take them up as they appear useful, and not because the church calender makes them salient. That might sound like reverse stupidity. It is. I am intentionally suppressing hypotheses which have been brought to my attention for the wrong reasons.
The line about Lent being scientific is cute, but really Lent is, to observing Christians, a time to practice penance, cleansing, and devotion. Which means that Lent and analogous ceremonies in other religions (Ramadan, Yom Kippur) provide data on the folk psychology of obedience and cleanliness! Let's explore.
The primary evolutionary purpose of disgust is in response to foods and scents which should be avoided because they could cause microbial contamination of one's body. Disgust drives us to avoid elicitors of disgust, such as dirt, wounds, corpses, bodily fluids and discharges (blood, feces, vomit, semen, puss, urine), unprepared foods, certain animals associated with those things (cockroaches, rats, flies, lice).
Not only does disgust cause us to avoid certain stimuli, we also often reject e.g. foods based on their past exposure to disgusting things, even when the offending odors, tastes, and sights have been neutralized. This is quite useful, because microbes are not visible to the unaided human eye and contagion is a real thing. It's also a potential source of cognitive bias. Some children don't want to eat food that they have seen touched by non friends or kin, even though cooking subsequently sterilizes it. I think a bayesian statistician might call that a spurious association that fails to consider the effect of cooking to screen off known sources of contamination. Presumably this applies to the other domains where disgust applies, which I'll address shortly.
Many religions thus have rules about which interactions between objects make them unclean, and what rituals of cleansing can restore cleanliness. Leviticus 11 is a beautiful source of zany contagion laws. Touch a carcass, and you're unclean, but only until the evening. Pick up a carcass, and you'll also have to wash your clothes. If a crawling or flying bug falls into a ceramic pot, break the pot, it can't be cleaned. Bugs with jointed legs are cool though. Feel free to eat crickets and locusts. Seeds to be planted can touch dead bugs, but water that you pour on planted seeds can't. Et cetera. And we've all heard the anecdote about doctors refusing Semmelweis's insistence to wash their hands before medical procedures, because a gentleman's hands are never unclean.
More generally, humans have rituals of purification that apply to both disease and sin: baptism with holy water, anointing (abhisheka to Jains and Hindus) with milk, butter, yogurt, honey, and oils. Interestingly, I don't know of any cultures that cleanse with alcohol, which is an actual disinfectant, unlike yogurt, which spoils easily. In addition to washing and smearing, humans use smoke and incense to cover odors (not an effective epidemiological intervention).
Next, Lent is strongly associated with atonement for sins through sacrifice. The more you suffer, the better you're doing. Christians promote a self-critial mindset, recall their past selfishness, injustices, defiance, and obscenities. They sit in little rooms with old men and confess their shame.They inhibit their impulses and addictions, which are basal, animal, and akratic. They practice celibacy, they fast, and they impose dietary restrictions, on i.e. meats, caffeine, candy, or baked goods.Sexual abstinence is performed both because sex is pleasurable, and because it is associated with perversion and depravity (spousal abuse, exploitation, rape, incest, masturbation, zoophilia, cuckoldry). Catholics temporarily redefine fish to not be a meat, which apparently fools God.
There is much concern for conformity to orthodox rituals, and for which behaviors are permissible or taboo. They devote their time to prayer, and focus on their reverence, obedience, and faith in the authority of their deity and its church.
Most of that came from a lecture by Pinker on taboo language and an article by Haidt on his theory of moral intuitionism. There are some other concepts which I associate with Lent that I'll list now, followed by lists of associated adjectives, on the hypothesis that important psychological traits have strong lexical coverage. "They" will refer generally to religious people observing periods of sacrifice, self-critical reflection, or obedience.
They have high standards:
diligent, meticulous, exacting, perfecting, thorough, high standards
The standards center around impulse control:
self control, discipline, restraint, mildness, moderation, conservation,
And denial of sensual comforts:
sober, ascetic, abstaining, austere, sacrificing, refraining, modesty, chastity,
And fear of supernatural authority:
deference, reverence, veneration, obedience, meekness, piety, humility,
They want to meet the standards:
drive, purpose, focus, intent, aim, motivation, determination, commitment, conviction, resolution, vigilance
Failure to meet their standards will be met with bad consequences, and is no casual, laughing matter:
solemn, stoic, grave, somber, serious, mature
They have respect for the virtue of attempting and or succeeding to meet their standards:
strength, resilience, tenacity, endurance, perseverance, constancy, persistence,
They endure their sacrifices willingly:
patient, calm, composed, abiding, constancy
And a few stray thoughts that don't have lexical coverage: Along with fasting and impulse control comes a desire to consume few resources and to not burden others, self reliance. Also a general disdain for personal wealth and material possession. Rather than promoting open-mindedness, flexibility to change, and experimentation, Lent enforces conformity to established traditions (which might be the rational choice if personal experimentation does not produce fruits commensurately with invested effort).
If you actually want to adopt a Lent-based rational tradition, consider some of those points.
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.