I've been rigorously working on plugging leaks that I've discovered in my game for the past month due to running bad resulting in a couple of big downswings. After a much needed upswing last week, I find myself in another big downswing and re-evaluating my leaks. For example, I notice I lose big pots when I'm in the blinds. Flopping 2p in the BB in a limped pot then value-betting a loose-passive player who ends up hitting his flush OTR. I also notice I play my TPTK/TPGK too passively when I'm not the PFR. I also find myself playing SCs and Axs OOP when I'm card dead. I've managed to plug those leaks I've mentioned but I'm still running bad. Then last night at the end of a 7 hour session I called down a drunk aggro who's been betting out with anything and lost a $700 pot when he tabled 99 and I had 88 on a 2 5 7 J 6 board. I blamed it all on running bad tilt but then I asked myself what was I thinking calling him down. I just thought he was bluffing and I was gonna play my hand as a bluff catcher.

I realized the biggest leak I have is that my thought process is flawed. So my question is how or what resources can I use to develop this? I feel that I've read so many poker books and watched so many videos but I can't seem to organize my thoughts anymore when I'm playing.

Any advice or maybe a book that anyone would suggest would be greatly appreciated.

Good job realizing this.
This is a HUGE first step.
If you are seeing these things then to be quite honest it should be a simple step to try and get away from the situation. Just don't do the things that you see your self doing that is wrong.

I know that sounds stupid and straight forward, but sometimes it's just that easy. For example, you talk about not playing your TPTK very passively. When you have those types of hands, make sure you think to your self, what do I have, what am I betting and WHY am I betting it. That's the real big part. Think about why you are doing what you are doing.

Also, it sounds like you are going through a down swing. Down swings are really tough to go through. A lot of times it's even harder when you think that you are good (and you might be don't misunderstand me) because you get a sense of entitlement. That you 'deserve to win' and that the fish 'can't keep getting lucky' and it leads up to making some bad plays.

It sounds like you need to take your time and think about your decisions during the hand, and decide why you are making those plays at the time.

OP - There are coaches, this forum, books, and videos. I locked the thread because it is too much like a blog and for anyone to give you truly good advice they'd need a ton more information than you gave. I suggest posting some problem spots you have and keeping up with the forum. If you put time into studying here it should pay off.