Ok I think I've changed my mind as to what was causing the issue, I think it's my Fender ABY box, I removed that and just had tuner, pog , muff and no weird sounds.
Seemingly on the ABY when channel A is selected, everything is fine, when it's channel B there's a loud hum even when nothing is plugged it and touching the unit changes the hum. So going to both creates the organy like sounds. So looks like that's the culprit and possibly some grounding issue with that.
I only got the ABY the other day so I've messaged the seller on eBay to ask for a replacement