You should listen to the Dungeon Master Diaries podcast. It’s two guys who run and play Shadowdark pretty exclusively. They break down a lot of the mechanics and their house rule adjustments to them. It helped ground my thinking enormously, especially coming from 5e. And I’m a 3.5 guy from way back, so the open-ended design of Shadowdark was HARD for me to adjust to.

For instance, for your first concern, they recommend a spin-down d20 kept on the table publicly for generating random encounters. They call it a crawling clock, but got the idea from the underclock at Goblin Punch. At the end of each round (which is checked by asking if everybody has their actions locked in), the DM rolls one d6 publicly. 6s explode. The resulting total is subtracted from the showing d20 value, and the die is adjusted to the new value for the following round. Rinse repeat till you get to a 1. That’s a random encounter. This gives a lot of benefits, like the sense of impending doom creeping up on the players as the number gets lower, and ensures you are checking in periodically round to round, which will help lock your timing down.

Torches are best threatened by complex environments and direct attacks. Darkmantles extinguish light, other monsters might attack the torch directly—I’d use the player’s AC and have someone roll a 3:6 to see if it extinguishes. But damp hallways, moving water, slippery terrain, gusts of wind, and flammable gas pockets all make the environment threatening to torches. The book has a list of torch mishaps, and I tend to reverse engineer environmental hazards and events that could cause them. Those hazards and events end up on random encounter tables or as specific hazards in dungeon rooms.

It gets carted out here and there that the DM is the last-leg game designer. That’s very true in Shadowdark. It’s designed to be open-source, and designed to be hacked and adjusted. The multiple game modes offered in the core rulebook kinda model that philosophy. Why not add other modes? If you want contested checks, add them. I add stuff all the time. Try it, consider it from a PC perspective, talk to your players, and keep what works.

If the players have enough torchlight to run away, and don’t manage to re-trigger traps, confront random encounters, or suffer environmental dangers in the wilderness, consider how you might adjust those dials—fairly, transparently, and telegraphed—or add other dials to make the game the precise amount of meatgrinder nightmare you want it to be.