This is what I get before and after generating the rig from the basic metarig
The only change I made was to position the generated rig on the z axis to align with the character.
I followed a few youtube tutorials, and usually, when they generate a rig it comes out with all the bones in the right place. No idea what happened here. Something about my setup must throw off the rigify algorithm. Any ideas?
I am pretty newb to this stuff. Sorry in advance if I haven’t included relevant information or something. I can update the thread in the evenings with new info if needed.
Not real sure what you did without a blend. You can always post one here https://pasteall.org/blend/ and give us a link. However, usually you have moved a rig in object mode and the transforms are not applied before you generate your rig. If that is not it, please post a blend.
@stilltrying Hmm, maybe it is the issue you describe. But I am unsure who to confirm if this is the case. (I thought that when you move something in object mode a new location automatically applied, but other things like modifiers need to be applied.)
Here is a link to the blend file.
https://pasteall.org/blend/3732086b96eb44e9b6d145bc51ac6867
Thanks for looking into this, appreciate it. Been stuck a few days now.
Yeah that’s all it is. Delete your rig. Go back to your metarig. Select it and control A to apply all transforms. Generate your rig again and your good to go.
In object mode. I was able to delete the rig, go back to the meta rig, select, control A, then I clicked Apply All Transforms. but when I generated the rig again the only difference was that it was aligned properly to the rig. 1/2 problems solved though 
I still have the issue of the bones in the wrong place, like coming out of the middle of the feet, pointing out of the body instead of up the spine, a few floating outside the body, etc.
@stilltrying
Did you see that on your end when you regenerated the rig? Or did the bones look normal?
Maybe you did something else different from me? Or maybe I am hitting a bug that only applies on my computer and not yours? I am on Blender 2.90.1 on Windows 10.
Would you mind sharing what version you are running? I could install that and try my .blend there.
Thanks again for the help.
I didn’t see that. Try a new blend file and see what happens. You may need to download a new blender if it got messed up. Just put in a metarig and generate it. If it is OK, then you had to somehow move a bone in the metarig someway to mess it up. You can also try to put in a new metarig and generate it and see if it is OK. Make sure all your transforms are applied before you generate it.
Thanks again for the troubleshooting steps here.
I created a new .blend and just added a metarig. Applied all transforms and generated the rig, surprisingly I got the same behaviour with the weird bones generated outside the body and between the feet.
I downloaded a second version (2.92), created a new blend file and also got the same issue.
Sadly, I didn’t have too much time tonight. Maybe I’ll go back and try some older versions of blender tomorrow. If you have any other troubleshooting ideas, please let me know and I can give them a try as well. I have a few other computers I can try it on as well. Mac, windows and linux. I guess I’ll just keep trying until something works 
Here are screenshots of the generated rig and a .blend from the 2.92 run.
Blend: https://pasteall.org/blend/dace869b43d044848cd9be81ea7adb1c
Are you looking in edit mode? Move to pose mode. Root is between the legs. What bone are you talking about?
Yes, I am looking in edit mode. Perhaps I am just confused about what an expected rig should look like. As it seems like the picture looks completely normal to you. So maybe there is no issue here at all in my new .blend file.
I was referring to these bones floating outside the body and pointing out of the body, coming out from between the legs and the spine.
Looking back the image I posted in the original post. You were likely noticing some other issues, (like the disconnect in the spine).
Okay thanks again. I feel like I should be able to start fiddling with a new blend file and figure stuff out.
Ok that’s normal. those are your pole target bones. They help IK figure out how to bend. You would use those to animate the angles you want the arms and legs to collapse (bend) at the joint when you animate. Normally they just hang out like the rig is. They normally are not visible in pose mode because the layers are not turned on. You can turn the layers on in the armature if you want to see them. There is a armature constraint on the bone that you can view, if you want to, that controls where the knee points using the big arrows with a driver. Basically don’t worry about it.
