So many questions! Such confusing organization!(1) To re-start or continue: If you've been away from the game for a very long time, I would recommend re-starting a new party. A lot goes on, and if you can't remember where you've been, what you've done, and where you may have stashed essential items, you're more likely to spend most of your time wandering aimlessly if you just try to pick up from where you left off.
(2) Ju-Ju Stones, Dragon's Teeth, Brimstone Nuggets, Deadman's Hair, etc.: All of these items, typically called "reagents" when you need to identify them, are items that can be equipped to increase your resistance to various types of magic/attacks. For example, Ju-Ju Stones increase your resistance to lifeforce attacks by 30%. These may be useful for beginning parties, but as each character can only equip one such item, and you come upon much better items later in the game (e.g., Amulet of Healing), the most common use for reagents is to sell them. (IMHO: reagents are a good candidate for "mixing" in any future CODS mods.)
(3) Party make-up: It's been said before, and I'll say it again: party make-up is very much a personal choice. ANY party can complete the game. It has even been done by a solo, unclass-changed thief. The BEST strategy for defeating the end-game, and entirely optional, Gorrors is simply to have a high level, or in the case of 1,000-eyes, a VERY high level (it's a 99 or 100-level monster). Of course, they can also be defeated at lower levels, it just takes more persistence and strategy.
(3A) Your party: end-game Samurais and Lord/Valkyries are nice: access to the best weapons and armor in the game. I recommend one Samurai and up to two L/Vs, as you will certainly obtain sufficient armor for these, and in a full party, this nicely fills out the front line.
Monks have the advantage of a naturally-good armor class. As you note, their magic is unimpressive. I often have a monk (or a character who has accumulated psionic spells) for role-play reasons.
Rangers: very good hit points. Some people pan the alchemist spell book, but IMHO, cloud spells are some of the best in the game. The reasonably-best armor for a ranger chainmail+1 or chamail+2, depending on your preferences. You get a guaranteed set of the first, and can obtain the second with only reasonable difficulty. As the character is elven and probably back-row, the weapon of choice will probably be the elven bow -- +1 regen and guaranteed availability. However, when I play with a back-row elf, I will usually make her a Valk and arm the Maenad's lance (same regen, better damage, but only limited availability, unless imported from Bane).
Bard: NOT a good end-game character, and no reason to maintain this class. It has poor hit points. START as a bard and change to some other class. You can still use musical instruments and still increase musical skill. Because end-game instruments can be very useful and may become this character's primary mode of attack, this should be a back-row character, if you run a full party.
Bishop: as you say, it is a personal choice. I never take them.
(3B) Racial choices: Again, this is a personal and role-playing choice. However, I note that in some cases, you use race-class combinations to maximize attributes (the mook-monk is the best example: the monk requirements tend to compensate for the mook's starting attributes, leading to a character that is 13-10-13-10-10-13-9 when first s/he switches to monk), in other cases you have not (fel-sam, dwa-lor). My own approach is always to prefer the mook-monk pattern, so I would go fel-lor, raw- or dwa-sam; elf-val is another good one, and there are others.