I am an idiot. I failed to do the basic tests with these units and deserve to be beaten and mocked!
Last night when i reassembled the unit i decided to put in a cdr of burncycle to make sure it booted up and worked. I grabbed a controller wondering if i can press play at the startup menu cause the cursor is right over play. It moved.
Right away i thought it was something i had done but then realized i was using the controller from my working 490 and not the controllers it came with or my spares. i keep all the controllers in a box.
I never used my controller from my working unit thinking the others it came with worked. So the only way to prove it was the controller and nothing i did to the unit was to plug in the second pal unit. The cursor also moved.
I didn't know these controllers could break down.
Played burncycle for hours in disbelief.
The 2 units worked all this time
Only problem is sometimes i have to open and close the cd tray a few times to make it bootup.
So ends this thread and thank you all for your help.
Let the party begin!!!
update:march 7
Now that i think about it the cdi 490 only uses the longer stick controller and the other gamepad and larger stick controller are not compatible. This could be why i was stumped with them.
Also i never disassembled the other pal unit but i did remove its socketed bios chip and turned it on. Same for the other unit. Its possible it did reset itself internally.
But im not sure if i ever used my working controller in the past. So maybe un seating the bio chip had no effect.
I have learned much from this and will clean and double check av cords and controllers before doing anything inside a cdi or any console. And try multiple controllers and accessories till i get the right one.