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I've only had to remove them once my engine was out of the truck, so pretty easy. This is not a process I ever want to do, but I would do it grudgingly.
They often break apart, with some pieces of plastic falling into the valve area, down the drain holes, and into the oil pan. Some may come out during the next drain, but the tiniest will get picked up and go through the LPOP. Being plastic, they won't damage the gears and will get caught either by the oil filter or the HPOP screen under the oil cooler. The PITA thing to do if you don't want that is to remove the valve covers and plug the drain holes in the heads. And that gives some ability to push the harness plugs out when also pulling on them from the outside.
There is a tool to help pull these, and some people wrap wire around the plug to help pull them out. Wherever you remove the harness, plan to buy a replacement.
Someone who has dealt with this firsthand should be able to give a better feel for the process. Hartwig would be a good respondent.
You need to make sure that you get the proper glow plugs for the model year!
ZD-32 (ZD32) or 4C3Z-12A342-A are current part numbers for your year model (shorter version: 04.5+).
(FYI) During the 2004 model year, the combustion chamber on the piston was modified (updated bowl design). Due to the design change of the piston, the glow plug was made shorter by 1.2 mm. If the longer glow plugs are installed into an engine with updated pistons, glow plug to piston contact will result, ending in potential catastrophic engine failure.
First check to see how brittle the harness and connectors are. There can be quite a bit of variability in this .............................. age, engine heat, past history (if any) of doing this job previously, aftermarket parts vs OEM, etc. If they are not too bad, I would absolutely go in through the fender well area. IMO this is just another component that will reward you if you never allow your engine to run hot.
I have an '06 also and replaced the harnesses at 100k miles. They really didn't need it at that time, but decisions like this at 100k miles have given me 150k MORE miles of trouble free driving. IMO (no proof), the harness/connector material was upgraded in later years as compared to the first year (2003).