You can run those two commands any time after embark, I would think. As to adjusting the sky limit, I have no idea... About reducing cavern layers - I know it's possible to completely wipe HFS from your world if you do it wrong... If you don't really mind that, then no problem. To increase the mountain frequency, I would set the erosion to a really low number (or even to "None") and then set the elevation mesh size to 2x2, and then for the elevation weighted ranges:
0-20: 1
20-40: 2
40-60: 4
60-80: 9
80-100:16
Note: You'll probably get a lot of rejects if you just do this, but eventually it'll settle down and gen the history. I would also suggest you double the elevation x/y variance. That'll give you more variety, and probably also give you the bonus of fewer rejects... I think. Haven't tested that in particular, but I know how it works.
You may want a lower mineral scarcity..... change it if you want it.
That ought to amp up the mountains significantly. Remember to set the final page of values to "None" - the "minimum number of ____ squares" values. You don't really need those in the first place, in my opinion, unless you're ubertweaking.
You'll want to bump up the evil in the world if you want to embark in an evil biome - do the same thing for the savagery mesh/weighted ranges as you did with the elevation and then go to the evil square counts and multiply those by 10...
I could just design it for you, I suppose, if you'd like.
EDIT: I realize I gave you a ridiculous amount of instructions there, so I went ahead and designed an example world. Take what you like, trash the rest - get it to where you want it. The caverns are all still in, I didn't mess with those. Medium-sized world.
[WORLD_GEN]
[TITLE:SKELE TAL]
[DIM:129:129]
[EMBARK_POINTS:1274]
[END_YEAR:250]
[BEAST_END_YEAR:200:80]
[REVEAL_ALL_HISTORY:1]
[CULL_HISTORICAL_FIGURES:0]
[ELEVATION:1:400:800:800]
[RAINFALL:0:100:200:200]
[TEMPERATURE:25:75:200:200]
[DRAINAGE:0:100:200:200]
[VOLCANISM:0:100:200:200]
[SAVAGERY:0:100:200:200]
[ELEVATION_FREQUENCY:2:1:2:4:9:16]
[RAIN_FREQUENCY:1:1:1:1:1:1]
[DRAINAGE_FREQUENCY:1:1:1:1:1:1]
[TEMPERATURE_FREQUENCY:1:1:1:1:1:1]
[SAVAGERY_FREQUENCY:2:1:2:4:9:16]
[VOLCANISM_FREQUENCY:1:1:1:1:1:1]
[MINERAL_SCARCITY:2500]
[MEGABEAST_CAP:18]
[SEMIMEGABEAST_CAP:37]
[TITAN_NUMBER:9]
[TITAN_ATTACK_TRIGGER:80:0:100000]
[DEMON_NUMBER:28]
[NIGHT_TROLL_NUMBER:14]
[BOGEYMAN_NUMBER:14]
[VAMPIRE_NUMBER:14]
[WEREBEAST_NUMBER:14]
[SECRET_NUMBER:28]
[REGIONAL_INTERACTION_NUMBER:28]
[DISTURBANCE_INTERACTION_NUMBER:28]
[EVIL_CLOUD_NUMBER:14]
[EVIL_RAIN_NUMBER:14]
[GOOD_SQ_COUNTS:25:251:503]
[EVIL_SQ_COUNTS:250:2500:5000]
[PEAK_NUMBER_MIN:12]
[PARTIAL_OCEAN_EDGE_MIN:1]
[COMPLETE_OCEAN_EDGE_MIN:0]
[VOLCANO_MIN:3]
[REGION_COUNTS:SWAMP:260:1:1]
[REGION_COUNTS:DESERT:260:1:1]
[REGION_COUNTS:FOREST:1040:3:3]
[REGION_COUNTS:MOUNTAINS:2080:2:2]
[REGION_COUNTS:OCEAN:2080:1:1]
[REGION_COUNTS:GLACIER:0:0:0]
[REGION_COUNTS:TUNDRA:0:0:0]
[REGION_COUNTS:GRASSLAND:2080:3:3]
[REGION_COUNTS:HILLS:2080:3:3]
[EROSION_CYCLE_COUNT:0]
[RIVER_MINS:100:100]
[PERIODICALLY_ERODE_EXTREMES:0]
[OROGRAPHIC_PRECIPITATION:1]
[SUBREGION_MAX:2750]
[CAVERN_LAYER_COUNT:3]
[CAVERN_LAYER_OPENNESS_MIN:0]
[CAVERN_LAYER_OPENNESS_MAX:100]
[CAVERN_LAYER_PASSAGE_DENSITY_MIN:0]
[CAVERN_LAYER_PASSAGE_DENSITY_MAX:100]
[CAVERN_LAYER_WATER_MIN:0]
[CAVERN_LAYER_WATER_MAX:100]
[HAVE_BOTTOM_LAYER_1:1]
[HAVE_BOTTOM_LAYER_2:1]
[LEVELS_ABOVE_GROUND:15]
[LEVELS_ABOVE_LAYER_1:5]
[LEVELS_ABOVE_LAYER_2:1]
[LEVELS_ABOVE_LAYER_3:1]
[LEVELS_ABOVE_LAYER_4:1]
[LEVELS_ABOVE_LAYER_5:2]
[LEVELS_AT_BOTTOM:1]
[CAVE_MIN_SIZE:5]
[CAVE_MAX_SIZE:25]
[MOUNTAIN_CAVE_MIN:25]
[NON_MOUNTAIN_CAVE_MIN:50]
[ALL_CAVES_VISIBLE:0]
[SHOW_EMBARK_TUNNEL:2]
[TOTAL_CIV_NUMBER:40]
[TOTAL_CIV_POPULATION:15000]
[SITE_CAP:1040]
[PLAYABLE_CIVILIZATION_REQUIRED:1]
[ELEVATION_RANGES:0:0:0]
[RAIN_RANGES:0:0:0]
[DRAINAGE_RANGES:0:0:0]
[SAVAGERY_RANGES:0:0:0]
[VOLCANISM_RANGES:0:0:0]