One thing this is going to cost you is time; not a couple of days, like a modern trip to somewhere on Earth; your beanstalk climb will absorb that. Not even a couple of weeks like a transatlantic ocean liner, but several years, like Marco Polo visiting China. So you're going to get to know your fellow passengers very well. Indeed, a psychological compatibility certificate might easily be a requirement for a ticket, as might a week in 'Big Brother' confinement conditions.
So, your marsliner is either built on Earth and lifted up to orbit by the space elevator (unlikely, since it will be enormous to hold the supplies needed for the trip and return voyage, plus its fuel, and anything to be delivered to the growing colony on Mars) or, more likely, built in Earth orbit next to the geostationary counterweight of the tower partly out of bulk materials from the moon or the asteroids, partly from prefabricated sections lifted up from the planet by the elevator itself.
In the latter case you travel up to geostationary in your smaller cabin, which will later be reused as an orbital craft: it is, after all, equipped with everything a low-acceleration spaceship requires except the drive and fuel; and they might well decide to attach that, anyway, while it's going up. It's only worth sending capsules back down when they've something to carry: biologicals you don't want to risk in Earth's atmosphere, crystals that can only made perfect in negligible gravity, alloys that won't mix if acceleration if pulling their components apart. The geostationary hub is the centre of a floating city, hotels and residences, mainly industrial but quite a lot the commerces that have flowered in every port from the beginning of history.
For this is a port; the port for a planet. Unhurried crewless solar clippers set their country sized sails for multi decade trips to the outer system, lunar ferries service the colony on Earth's nearest neighbour, bustling service craft circle the planet repairing and replacing communications satellites and, once or twice a year a big manned ship sets off for Mars, or the moons of Jupiter.
The ship can wait a long time in stable orbit, but when it contacts the outward pointing spike of the orbital tower (which has to exist; it is the centre of gravity of the structure that is in geostationary orbit) and the motors start to pull it out, father from the Earth, where its own mass will fling it ever faster away, accelerated by the Earth's rotation way over escape velocity, timing becomes to the fraction of a second. And there is a detail here that most space elevator fanatics ignore; this extra speed, this acceleration has to come from somewhere; and the force in this case is from the tower itself, at right angles, slowing the orbit a tiny fraction. Only a tiny fraction, because the tower masses many times what even the massive ship does, but every time it flings something out into the dark the tower needs to be sped up by a reaction motor to keep it stable. It is not free power; even the capsules climbing to orbit are sapping tiny points of orbital speed, which need to be compensated for.
Now we come to a choice point; either the ship can slow down into a Mars orbit, and use small, simple landing craft (or an orbital Mars tower, though you'll need quite a lot of visitors before that becomes economic), which means, with a reasonable power engine, starting braking almost as soon as you've finished your release of the tower, or using more sophisticated craft for landing, big enough you can probably spend the entire voyage in them, and the most massive part of the ship firing them backwards and not slowing down at all, but settling in for a nice long circuit of the solar system (if it only goes as far out as Hailey's comet that's a seventy-five year cruise) Faster, but more wasteful. And a lot more expensive. Atmospheric braking, with something the size I'm considering, is not really an option (and Mars' magnetic field doesn't lend itself to eddy current braking; you could make the engines a whole lot more powerful but this would require more reaction mass, or a brand new technology to accelerate it (not impossible).
However, even the fast trip would be several months, and the trip back home a lot more, unless there was a Mars orbital tower, too. You can't expect the round trip to be less than a couple of years, even if you don't land on the planet (which would be silly). Even with the chronicles network beamed straight to the ship, that's a big lump out of a young person's life, a long time spent with a very limited selection of company. Particularly on the trip home, so colonists would have it easier than tourists. And as light speed delays grew, virtual conversations would get more and more detached, less and less personal.
As regards your mineral eating bacteria, not impossible, but there would have to be a reason why the de-energised substance was recharged; vulcanism as in the deep ocean rifts, ultra violet light cooking the surface layer and dust convection currents carrying the newly energetic matter into the depths (not impossible that, but a bit incompatible with caves), something. Remember, their has to be enough energy to drive the entire ecology.
On the mining front, iron is at the bottom of the energy curve and is going to be cosmically common, so lifting it out of Mars' gravity well doesn't sound economic; far more efficient to seek out a nickel-iron asteroid (the number of nickel-iron meteorites suggests this would not be particularly difficult). What you need is something that will only form in a gravitational field, or in the presence of carbon dioxide, or something. Some kind of crystal, perhaps? All the elements are likely to be cheaper to obtain in free fall, or extract from seawater, or something. Think of the quantity of steel used daily on Earth; now try and work out an economically viable way of transporting even a fraction of that mass (not that iron smelting doesn't put huge quantities of cee oh two into the atmosphere, but it's important only because of the immense tonnage involved.
Sorry about the length of this; I was without internet connection for two days, and it 'just growed'