A friend of mine has a 2006 Hiace with a 2KD. After it's been sitting for anything over an hour or so, when you start it, it won't idle. The revs will fluctuate by a couple of hundred RPM and if you don't give it some throttle it will stall. If you feather the throttle for the first 5 seconds or so it sorts itself out and runs fine.
He just had it serviced (not at Toyota) and they suggested getting it read with a scan tool, but it sounds more like a fuel supply issue to me than electric. He also heard from someone to fit a check valve in the supply line to stop fuel draining back to the tank, but basic diesel theory suggests if that was happening it would stall regardless of what you do with the throttle?
Any suggestions chaps? Also, I haven't looked for the diagnostic plug on it, but does the trusty old paperclip scan tool work on these?