So, this is my discovery and theory on what led to the problem...
-First and foremost it appears the board is damaged. TH1(P0.23) and TH3(P0.25) are no longer useable.
-A few months back I had a glitch that skyrocketed my hot end up to 395deg which I think this is where my problem originated as I now believe after some investigation that this led to the breakdown of the two PFTE sleeves on the thermistor leads. Although much care was made to ensure that there is no movement in the first 3" of the TH and heat cartridge leads I feel the small vibrations in the end effector ultimately finished off the PTFE sleeves allowing the leads to contact the block and short out after the hot end would get up to temp.
-When I first noticed an issue I performed a quick test by swapping the bed and hot end THs and noticed the problem stayed at TH1 port. I chose to reassign the pinouts without investigating further after seeing that port TH3 was reading ok. After printing with the new configuration for approximately 2min the printer failed again causing port TH3 to also become damaged. This led me to perform a full investigation into the problem.
-I've since installed a new TH on port TH4(P0.26) and all appears well now but I have lost two ports to the ordeal which sucks.
All that aside I am considering moving up to the Smoothie 5xC. I do like the MKS SBase but the hardware does have it's moments ad although it is relying on Smoothieware FW I'm not totally convinced that the two are fully compatible as minute as this problem may be it does have it's moments. My only issue with making the leap is spending $200 on a $350 printer...If I don't do the upgrade for this printer it will definitely go in scratch build delta...