I have always been a manual installer going back to Morrowind. I have installed mods for Morrowwind, Oblivion, Skyrim, Fallout 3 and New Vegas and have never had an issue I couldn't resolve, until today with Skyrim. While I may not have needed to drop a nuke on all game files, I went ahead with it anyway.

So, my question is, should I reconsider using a tool for installing mods? Excluding Skyrim, I've run 50ish mods on the other games mentioned without ever feeling the need to start from compete scratch. Skyrim I was up to 75ish, and wasn't the most careful today when installing approx 5 more, including SKSE for the first time (I've used script extenders for NV and Oblivion with no issue).

That said, is it worth trying a mod tool when using excessive numbers of mods? Or should I simply have been a bit more careful today, and not tried adding a few more while in a cloudy haze of being sick? If you intend on bashing me for only having done manual installs before, don't waste your time. I'm looking for intelligent discussion on manual vs mod tool installation.

I, of course, suggest and encourage using Wrye Bash to manage installation, but you seem to be pretty experienced, so, you know, do what you want.

I'd say the real question is, what went wrong? And why couldn't you solve it? Without knowing the answers, I can't tell if having a mod manager would have helped you or not.

Cheers!

Booting via SKSE gave me a straight lock ups at the title screen before the options appeared. Even after closing Skyrim via task manager, my CPU was still running full tilt until I rebooted it. This happened a half dozen times before I decided to wipe out everything. Perhaps I just need to download the latest versions of everything I had been running.

Well, hard for me to guess what was going on there. There's nothing inherently different about Skyrim or SKSE than any of the other games. Sounds like you're experienced enough to figure it out. But, for what it's worth, here's the case for Wrye Bash:

It allows you to manage the install order of mods. So, say you install mods A, B, and C, all of which contain loose files and all of which overwrite some of the existing files. If you realize after installing that you would prefer it if mod B overwrote mod C, with Wrye Bash you can simply move the installs. The program remembers all the loose files and which goes with which mod. If you wanted to do that manually, your process is quite a bit more exacting and time consuming.

In addition, Wrye Bash allows you to create a bashed patch, which allows for merging of leveled lists, so that one mods changes to a list do not have to completely wipe out another mod's, but they can both have their content show up in the game. You simply can't do this with a manual install. You can do something like it using TES5Edit, though.

Make sense?

Huh. Well that sure does sound pretty handy. Perhaps I will give it a try, though starting clean with a manul run again, when I pretty much know what I like from the mods I had installed would make the manual process easier, down the line when adding more that would be a nice feature.

I recommend Mod Organizer: http://www.nexusmods.com/skyrim/mods/1334/?

Or as gothemasticator said, Wrye Bash: http://www.nexusmods.com/skyrim/mods/1334/?