While you try that, I'll start working on this post to cover what's what.
Edit -
While this WinDroid tool is nice and all, it's probably obscuring a lot about rooting your phone and putting you in a guessing situation, so let's fix that.
There are three required steps to rooting a modern HTC and a fourth optional one.
1. Unlock bootloader with HTCdev.com - which leaves encrypted signature security intact, aka, s-on.
2. Install the supported custom recovery for the model - in our case, TWRP.
3. Obtain root by using TWRP to either flash a superuser package or by flashing a rom that already has that baked in.
Superuser (same exact thing as admin privileges on a PC) consists of two parts - a binary bit under the hood and an apk that you use to control root access by other apps. The superuser apk is the bridge between that superuser binary and the other apps that want root access.
The best and comprehensive superuser is SuperSU and here's where you can get it from -
http://download.chainfire.eu/supersu
There are more basic superuser packages and those are popular. The SuperSU from the Play Store will work with those and install itself over them, replacing them. If such a package wasn't there in the first place, the SuperSU app from the Play Store alone is useless to you.
But - you can always grab the flashable zip package from that link above and apply it, it'll give you the whole deal.
If you want to do that without changing your stock rom that you are presently using, do that.
Goo Manager may have failed you, even with the right instructions. It happens. It's happened to me.
To be completely prepared to handle your rooted phone, I recommend that you install our Mini-SDK, that allows you to manage things directly from your pc with just a few simple commands, without something like WinDroid trying to help.
Here's where you can get TWRP -
http://techerrata.com/browse/twrp2/jewel
Here's the link to the latest 2.6.3 version -
http://techerrata.com/file/twrp2/jewel/openrecovery-twrp-2.6.3.0-jewel.img
Here's where you can get our Mini-SDK -
http://androidforums.com/faqs/443072-adb-guide-updated-2013-05-21-a.html#post5389081
Follow the directions, unzip and put it in a C:\sdk-tools folder.
Open a dos/command window, here's how if you're not sure -
http://pcsupport.about.com/od/commandlinereference/f/open-command-prompt.htm
Plug your phone in to a USB 2 - not 3 - port on your pc.
If it says you need drivers, use these -
http://www.htc.com/www/help/htc-evo-3d/#download - but if you installed HTC Sync, then you have the drivers you need.
To flash TWRP -
1. Using your file explorer, go ahead and move the downloaded openrecovery image file to the sdk-tools folder.
2. Open the dos/command window.
3. First, get to your folder -
cd C:\sdk-tools
4. On your phone, turn off what it calls fastboot - main settings, Power,
uncheck Fast boot.
5. Get your phone into fastboot USB mode -
adb reboot bootloader
5. After you're in fastboot USB mode, do this to install TWRP -
fastboot flash recovery openrecovery-twrp-2.6.3.0-jewel.img
^^^ Notice that that last file name has to match exactly what you downloaded - you can confirm that in your file explorer on your pc.
That's the sure fire way to update TWRP as new releases happen.
Once you have a good TWRP, go ahead, put that SuperSU.zip from earlier onto your sd card (internal or external), and flash that from recovery.
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Whenever you flash a new rom or whenever you have any trouble whatsoever, go into TWRP, Wipe, Advanced, and clear cache and Dalvik.
Doing that and cleaning app caches (a topic we'll save until after you get everything else squared away) will solve your slowdown problems too.
For things as confused as your phone got (not your fault, I really suspect a bad TWRP flash here a whole lot) - go ahead, do the factory data reset.
If you want to save what apps you have first, along with their data, you can use Titanium Backup (once SuperSU is installed) or use the one I do, it's easier -
https://play.google.com/store/apps/details?id=com.rerware.android.MyBackupRoot
- and then restore that backup.
So long as you don't mind repeating some setups and doing MyBackup Root saves and restores, you can factory data reset any time you like to untangle your phone - and personally, I'm a big proponent of that, it does a lot of good. So much so that it's the default wipe in TWRP these days. But - you can do it from your phone settings - just don't erase your sd card areas.
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When you're all squared away, I'm going to want to talk to you about that fourth optional step I mentioned earlier for rooting - getting rid of s-on security so you can manage updates to your radios and install kernels easily and so forth.
But first, let's get you all squared away on the basics first.
Hope you don't find the details offensive, I thought it would save time to just lay it all out on the line for you without any assumptions because my schedule - as you've seen - is a bit spotty.
This post has everything in it you'll need and I'll check back as soon as I can.