Thank you for the app notes. I looked through them and didn't really find what I was looking for.
From everything that I have read, using two ADC modules simultaneously should not effect ADC results. However, it seems that they do if you trigger them too close to each other.
I want to make the point that I am currently using FTM to trigger a DMA request to write to ADCx->SC1[0] every 4us to trigger a conversion.
Originally the set up was a single FTM channel would trigger a single DMA request to write to ADC0->SC1[0], then the DADDR would update to the ADC2->SC1[0]. Since then, I set up a new FTM channel and DMA channel that would operate specifically with ADC2. So now I have an FTM channel that triggers a DMA channel to write to ADC0->SC1[0], and an FTM channel that triggers a separate DMA channel to write to ADC2->SC1[0]. I have found that separating the FTM CnV for the two channels by about 2.8us gives me the best results. The question is why 2.8us, and why did I have to separate them in the first place?
There were also two separate DMA channels that will be triggered when conversions are completed. One DMA channel triggered on ADC0 COCO, and one DMA channel on ADC2 COCO.
I only bring this up because everything I read says that ADCs running in parallel should not interfere with each other. So that brings the question about whether it has to do more with my set up then the time between ADC triggers. Could DMA channels be taking priority over others, and that is somehow effecting the results of ADC2?