Faulty SNES: Very weird issues, Plz help!

I have here an original SNES SHVC-CPU-01 ( the one with separate sound board and BA6592 encoder) and it has a very weird combination of issues.
-Controller 1 does not work at all, controller 2 works at least partially.
-Some games do not work at all.
-Some games will crash at specific points.
-Some games have weird glitch. ( like losing picture )

The post is a bit long because I already did a lot of tests on it and I will describe all I did.

I got it from a junk lot, which is how I get a lot of my hardware.

I cleaned its cart connector and tried it and it worked with two games I threw at it so i though ( cool, another one saved ). I then tried a few experiements on it, nothing really serious. I tried the capacitor fix for the Vertical Bar and I briefly connected the video encoder to my experimental component mod ( which is on a breadboard ) and saw that it worked ( despite it still needs adjustment). I do not recall doing anything stupid to it. Just some basic connections to test mods and the console was seemingly working and cooperating all the time.

I proceeded to put the console back together and decided to first play some games with it. This is when I discovered the Initial problem. Controller 1 did not work at all. ( I had not tried controller prior to this)

I made a thread on NesDev about it http://forums.nesdev.com/viewtopic.php?f=5&t=10619

- I tried different controller
- I tried different front daughter board.
- I checked all connections between the two boards.
- I checked the default logic state of all the controller board connections with the CPU, I used the SNES schematics to know where to measure.
I have the same results as with a properly working SNES.

All the time I was only playing the few same games. Which all seemed to work beside the Controller issue. But then I tried more games and discovered many have issues.

Contra 3- No video after intro but sound works.
StarFox- Lose video at some point during Intro.
Zombies ate my neighbor - Not working at all
FFVI - All looks good
DK country - all looks good
RnR Racing all looks good
Darius Twin: Crashes at scoreboard or when trying to start new game using controller 2
Pocky and rocky - Hard crashes in a blaze of graphical corruption during the intro. ( always at same spot )

Here is a list of all I tried next.

-Testing power rail voltage ( 4.98v)
-Trying with a different PSU
-Trying with a Stronger PSU ( A genesis model 1 with a temporary AC adapter input soldered to the board )
-Trying with a different Sound board from a perfectly working SNES SHVC-CPU-01
-OCD level cleaning of the Connector
-Replacing the Connector with a know good one.
-Reflowing all the CPU pins
-Reflowing of the Regulator


It still does the same bugs all the time at the same places.. I am a bit clueless but I think I will try a full recap next.
However my intuition is that it will not work as the problems are too specific. And I do not think bad cap should affect controller 1 functionality as the controller is basically hooked up directly to CPU.
My feeling is that the CPU is failing, but I could be wrong.

Any help or idea is welcome. I really hate it to call a console borked. Im a bit OCD about fixing them.