The first one is an engineering problem. If the mass of the cable is immensely higher than the mass of "whatever it is" then it simply doesn't matter. High efficiency (ISP) engines unfortunately stereotypically output very little thrust, while high thrust engines stereotypically waste fuel. So rather than hoisting something heavy in only 9 minutes using incredibly inefficient engines, hoist it in a couple days and then using super efficient engines very slowly get everything back into place. Basically you shatter the old ISP vs thrust tradeoff by immense capital expense.

The second problem also frankly doesn't matter much. Aerobraking is cheap and efficient. I don't remember the specs but it scales pretty well, even when small, such that one pound of re-entry vehicle can land something like 20 pounds of "stuff" if you do it right, so rather than building a second elevator you simply "give up" on 5% of the first elevators capacity. Weight of heat shield is immensely lower than weight of fuel to get up there so don't even bother with reusable shields. Also once you get something up there, you should never return it with the exception (possibly?) of people. So keep a stockpile of shipping crates of re-entry capsules up there and never take anything down. Ever. Except maybe emergency medi-vac. If it costs almost nothing to get it up there, send up a solar powered foundry and a solar powered machine tool plant and start squirting out a stockpile of rough spare parts and panels and the like.

As for the edit, the hidden assumption is the cables "have to be" side by side. However the fuel cost to travel along an orbit is basically zilch compared to getting up there. And the materials science concerns of basically building a cablecar elevator are limited. So if you really, really insist on installing a "down" elevator, simply up the "up" in Africa and the "down" over south america and if you still manage to tangle them, you must have totally screwed up beyond all recovery anyway.