1. Attacks are always made using contributing stat, depending of the weapon or classe's main stat for spells : for example using a melee weapon will use your STR modifier (so +2 on your roll for a 14-15 str), while ranged weaponry usually use your DEX modifier instead ("finesse" weapons too).
Spells are always cast using the main stat contribution, depending of the class : INT for wizards, CHA for Warlocks and WIS for Clerics.
Your attacks are 1D20 + Your "gobal"proficiency bonus (+2 at lv 1-4, then +3 and so on) + You main stat modifier (the one with a star on it).
To resist some spells (the ones with "attack/save" line), targets have to make a saving throw, based on the listed stat, using their own stat (for example Sacred Flame use the opponent DEX modifier + their proficiency added to their D20).
Your spells DC (difficulty class) is equal to 8 + proficiency + main stat modifier. so with a 16 WIS, giving you a +3 bonus, it's 8 + 2 + 3 = 13.
To resist (if able), target have to roll equal or more on a D20 + proficiency + their stat modifier.
So sacred flame is not very efficient against targets with high DEX (for instance, 14-15 DEX means they have to roll a 9+ to cancel the effect. Many spells can be reduced by a saving throw like this, using written stat.
2. There is currently no limits on long rests, I'm not even sure there is like a "timer" for the main quest (like after X long rests - days - your tadpole kill you) or anything - yet. :p
3. Mostly for roleplay purposes, like finding only food in cellars or dishes in cupboards. Magic weapons and armors are very rare and costly in D&D lore, and pretty much all weapons are somehow "standardized".
You will never find "quality" levels for gear unless said gear is enchanted or specially crafted (like Laez'el starting armor).
Keep stuff you find and sell them early on to avoid being burdened (you can only carry double your max weight).
4. Percentage is chance to hit, yes, and as explained on 1., you have a hit, then the saving throw of targets (is able to resist or halve damage/effect on most spells).
D&D is like that yes. Dont neglect helping/preparation spells like Guidance, Bless and Bane for instance.
Having higher position or other effects (hiding, hitting sleeping target) can nets you great benefits : advantage on roll (by higher position for instance) means you roll twice and keep the better result.
Disadvantage works exactly the opposite (like when in close combat you have disadvantage on ranged attacks/spells).
