Decided to hardwire the SDRAM clock back to the master OSC again.. and its booted up fine (need to do more tests)
This was the clocks PLD driven..
BLUE = CPU clock (50MHz)
YELLOW = SDRAM CLOCK (100MHz)

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Master OSC driven..

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Not massive change.. but clear something has changed on the rise and fall... More voltage output as well.. Those changes are enough to make or break it it seems
I mean maybe the timing report wasn't lying afterall ... (max clock)

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EDIT:
Now with about 250R in series with the clock...

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GB6 ran fine now as well..
So i'm leaning towards the PLD can't drive 100MHz SDRAM clock reliably now.. I mean it struggles to even hit 2v p-p a lot of the time. The min voltage on the SDRAM inputs is 2V !
Its running YAARTTT.. Will leave it on for a bit and see what happens now...