So starts fine, after about 1 minute of running I lose fuel pressure, won't start for about 30 seconds then I get fuel pressure again and does the same thing (doesn't matter which tank I have selected).

I dropped the fuel line right before the high pressure pump into a bucket, sure enough after one minute of running it stops spraying into the bucket (high pressure pump keeps running off a gas can), so I know it's a problem before the high pressure pump.

I really thought it was electrical but I checked the fuses, fuel relay and selector switch. I there anything else I should check before a start pulling lines to check for clogs / pulling the bed off?

Oh and I replaced the low pressure pump in the front tank about 500 miles ago

 

That truck has the dual function resovoir on it, I'd suggest you have a look at that next.