Well, I'm back here again.
This time my issue is rough idling. This didn't start till a day after I cleaned out the EGR Ports to fix the P0401 code.
Though I think I might have an idea what the issue is but I'm posting to make sure.

When I was trying to get the EGR off (and failed since one of the nuts got stripped) I got the "clever" idea to move the Throttle Body a bit to try to get the nut off.
I unscrewed the nuts from the TB and lifted it up and moved it a bit to the side. This was probably the huge mistake I did. I heard the gasket move around a bit but regretting the idea I put the TB back.
After that day I haven't had time to myself and try to solve the issue until today.

I used the search function for a guide on how to remove the Throttle Body for cleaning but to no avail. ):

If someone knows can you please link me to the guide or post step by step how to do it? I would really appreciate it. That's the last time I try one of my "clever" ideas that ended up being stupid mistakes.

 

You may want to reset the ECU by pulling the 7.5 amp backup/radio fuse in the engine bay fuse box. That solved a rough idle when I messed with my throttle body on my 95 accord.

 

I'll try that then.
Also, I realized that I goofed, I didn't tighten the nuts on the TB all the way.
That probably didn't help at all.