Happy trails (off road) to you. As you can see by my avatar I have an M109 which I bought in 2007 to turn into an off-road camper. It, too, is a '66, BUT it is non-turbo. It has a hard time getting into high gear at 5280 ft. elevation, so I won't be taking it to the mountains. Yes, I worked on it but only improved it slightly.
About plastic fuel lines, I believe you should replace ALL of them. When I disabled my FDC according to the published instructions I found that they were too brittle to bend the way they showed, so I changed all of them, believing that I didn't want anything left that was so likely to break. Any rubber or plastic on a 50 yr. old truck probably needs replacing, such as brake cylinders, seals, etc.
However, all my attention has been diverted to my M923A1, which also lacks a turbo, but reportedly does ok at altitude. It's an '84 and also needs lots, probably all, rubber replaced. I plan to bob the 5 ton and put the 109 box on it. If I move the spare and muffler and position the box as close to the cab as it is on the deuce, the single axle will come right between the 2 cutouts for the duels on the deuce.
About your M109, they have a thin layer of steel under the plank flooring which is probably rusted out. My truck came from the Arkansas NG and did one tour in Iraq. They put down a 5/8" layer of plywood. Several others on SS have fixed up 109s and there is a lot of good info. I see that you have been an SS for six years, so you probably know.
Good luck and I'm glad to see that you're taking preventative maintenance seriously.
PS About grinding between ranges, first you have probably had your truck out-and-about more than I have mine, so you are probably more of an expert than I. That being said, I have driven and worked on 4x4s for decades and they often have the same shifting ranges problems. This can be a serious problem if you are stuck in a mud hole before you go into low. I always try to be moving a little, about equal to a slow walk as I shift. The reason is that the transfer case has no synchros and often needs a little coaxing. If you are stopped, the gears aren't likely to be lined up. You can let the clutch out a little while it is in neutral, put the clutch back in and quickly shove it into gear. That will get one side of it moving. Just DON'T be putting torque on it while they go into gear or you might pop a tooth. Dentists for 6x6s are expensive.
