Help out a Mod virgin!
biffyclanger
Member Posts: 216
Just read the BG2EE compatible mod thread. So many options its making my head spin. I wonder what people here run with and which components they consider essential and if there are mods you strongly recommend I'd like to hear why. I've not had the best of luck with mods so I am a little bit reticent but hopefully you guys can convince me 
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Ascension
Restoration Project
Colors of Infinity (Quest mod series)
http://www.shsforums.net/files/category/106-colours-of-infinity/
Those are my favourites. the content fits very well in the vanilla game
Other than that, I'd say BG2 Tweaks is standard in terms of making slight gameplay adjustments to your liking. Unfinished Business restores some cut content. And that's about it for me - NPC mods are hit-and-miss, but if you're looking for one or two to try out, I'd recommend looking for characters who suit the party you're putting together.
Lately, though, I haven't been installing published mods at all; I've been working on a conversion to 5e rules, and that's about all I have energy for when I'm not at work.
BWS uses portions of the BiG World Project (BWP) -- bug fixes, language packs (translations and typo fixes) and install streamlining (e.g., some mods do "biffing" - compression - at the end of their installation, and the BWP removes these "biffing" actions from the individual mods and instread does "generalized biffing" at the end of the entire installation). BWS does not use BWP's install script for EE games.
The core goal of BWP is to maximize compatibility between whatever mods a user wants -- whether it be 3 or 300. It does this by recommending an installation order and by providing patches (via the BiG World Fixpack - https://github.com/BiGWorldProject/BiG-World-Fixpack) that can be applied to mods to solve compatibility issues (in addition to bug fixes) discovered through expert analysis and reported by users.
tl;dr - BWS is a Windows tool that assists with mod selection and installation; BWP is an installation guide (PDF) plus a collection of patches and scripts (including an install script that BWS does not use for EE games) that improve game stability for whatever mods you use. BWS uses some aspects of BWP but provides more user control.
SR
SCS
Ascension
That's my personal non-negotiable baseline. Certainly more challenging than the original game, but not necessarily crazy difficult (unless you want that; I do).
BGTweaks
Has a lot of convenience options, and borderline "cheats" that you can use at your own discretion. Includes things like minor cosmetic tweaks, party AI scripts, multi/dual class for all races, romance multiple characters etc. etc. Completely modular, meaning you only take what you want to take.
Quest mods: Tower of Deception (can be hard at low levels), Dungeon Crawl (some OP items, a robe similar to RoV to have 2 fast casters in the party), Back to Brynnlaw (some OP items, but nothing more than what you find in Item Upgrade), The Sellswords ( and there you find real OP stuff, like 10 Protection from Magic scrolls, that you can choose to buy or not) and last but not least Eilistraee's Song.
Each of those imo is well written, at the level of an official quest. Some of them add too much XP, and if you install many quest mod you will anyway have more XP, but you can install a mod to slow down XP rising and balance or just enjoy your overlevelled toons.
Do I need to reinstall SCS for it to work on these mods btw?
https://forums.beamdog.com/discussion/23726/bgii-ee-compatible-mod-list/p1
I have found, despite what is said by the mod-makers and various gamers, that my modded games are the edit:MOST bug free if I only do one clean install at the beginning of a new game. Even the G3BG2Tweaks, which is arguably the least buggy mod out there, plays best on a clean, one-time install.
That said, I am not sure how to best answer your question. You may not need to re-install SCS. However, did you install something out of order? If so, you may experience some bugs during play. And, if you installed out of order (which from your posts it seems that you did), it is possible that a file which SCS needs to use is now changed by a mod you installed after SCS. In that case, re-installing SCS will not do anything because it will still need to access that changed file.
Modding the game is the best way to enhance your gaming experience. Unfortunately, it can also come with some headaches for the uninitiated. My advice is just keep playing, which is what I did last time I installed out of order. It may be that you won't encounter any game-breaking bugs, and why completely restart your game on the off-chance that you might? If you do encounter some nasty bugs, you can just restart then. Make sure that, if you do re-start, that you modify a clean install only once in the correct order, using the thread that I linked above. That will give you the best chance of playing bug free.
About Dungeon be Gone, before intalling it try the Chateau Irenicus component of Tactics Mod.
Is the less cheating, maybe don't cheat at all, but is something that imo is worth to be experienced at least once (when you have become a strong tactical player, otherway is just a utterly frustrating nightmare).
About Dungeon Crawl in the second floor of the Dungeon, just after the blinding trap, you meet some people who ask you to kill a Beholder. Did you kill it? Well.... a lot of fun lost.
Try to talk to him, he is a very polite guy, and a shopkeeper, he and his friend has the good stuff.
Hope you have a save before it.
Too bad that TOD is not EEcompatible, imo is the best from the tactical challenge point of wiew, nothing impossible if you go there at the appropriate level, but designed very well. In the short time of a single quest 3 riddles to solve, Shadows whith their S. Lord, a strong demon (that maybe in my setup was enhanced by tactics), a lich, a Marilith, stronger than WK ones, an area filled whith stong lizards, Salamanders and lizard casters. And, when you think is all done, a lot of time after is all done..... surprise: a strong F/M, a real one, that use magic and mlee, like or better then your PWG F/Mages. AFAIK the only enemy F/M in modded or unmodded BG2.