Its a 2007 Yamaha 4 Stroke (F50FET). The engine went perfectly for the rest of the day, was just at the start. Engine has 78 hours on it now and had a full service at 50 hours.
I think you may be onto it with the air lock in the line. The boat was in the drive in the sun the day before I went out. I set off at 4am this morning so the tote probably had a bit of a vacuum on it prior to me disconnecting and filling it up. I didn't prime the line prior to setting out. There is also a large water trap on the fuel line that may also have helped push fuel out of the line.
All the shop did was add the oil, I drained the old stuff prior to going, looked clear and clean (not see through, but not milky). I drained it for a good hour prior to heading down to a local yamaha dealer who pumped it fill from they're bulk tank (pumped it till it came out the top fill hole, then did two more pumps into it).