I'll try and address each question and let you draw your own conclusions.
Do you know what type of fuel you are getting at the ranch from the supplier? If you get an 08 or newer car I'm almost certain they will require Ultra Low Sulfur Diesel (ULSD). Someone else confirm or prove me wrong.
The proximity to a VW dealer is not necessarily a huge issue. It seems a large number of VW dealers don't know how to properly service a TDI anyway. VW dealer service in general also rates pretty low in national surveys. There is a trusted TDI mechanic list on the site. Look thru it and see if there are any trusted mechanics in your area. Contact them. If you feel good about them that may solve most of your issues besides warranty work. If you rack up miles fast, you may be out of warranty in a year anyway. You can order VW parts at 20% off standard list at
www.1stvwparts.com shipped to your door. There are many trusted vendors on here as well. While my 96 Passats have much lower production than the Jettas, I find almost nothing is ever in stock anyway even in Dallas at the nations largest VW dealer.
Electronic controls: How old is your diesel truck? Unless it's an old 6.2 or 6.9 diesel, it probably has just as many if not more electronics than the TDI. The 96-03 TDIs are really pretty simple electronics wise. Not really any worse than a similar era gasoline car. The 08 up cars are certainly more complicated. Someone else will have to comment on the 04-06 cars. I started with simple carbonated cars. I found once I learned a little about fuel injection that they were far superior vehicles and dramatically more reliable and less maintenance intensive. I feel the same bout electronic turbo charged diesels. Far superior and the electronics don't cause much trouble. The 2 hassles I see on a TDI is the injection pump MUST be rebuilt by a certified rebuilder. So either it comes from VW or the shop in Oregon that can do it. The other is diagnostics/maintenance. It basically requires the shop or you to have a VAGCOM. Even a simple timing belt job requires this to be done right. Very few independent shops have one.
Ground Clearance: I have many friends here in Texas with rural ranch property and have had no issues with cattle guards, county roads, etc. I often go down gravel roads and some forest service roads as well. If you are on pavement I see no issues. Graded gravel should be no problem either. We regularly go up a very rutted steep unpaved driveway. You have to be careful and choose your line to avoid bottoming out but the car makes it up and has for years.
Wear out? What does this mean? OK, the clutch pressure plate broke at 351,000 on the sedan. I guess that counts. Actually the automatics are not known for their stellar longevity.....100,000 miles is not an uncommon failure point and they are expensive. But you want a manual anyway. If you care for your vehicles and they don't rust out I see no reason a TDI shouldn't make 400,000 miles. Really can't think of a TDI engine failure that was not timing belt related. Don't go over the timing belt interval, use quality German parts and have a TDI specialist do the belt and you should have no issues.
Injectors- Someone else will have to answer.
Practical- I find it very practical due to the low fuel cost and tremendous range. The only headaches have been maintenance related due to incompetent dealers and independent shops coupled with how hard it can be to find a competent tech. Parts prices for the Passat have been more expensive than Ford and Honda but really no more than Toyota.
Economical- They hold value very well so that helps lower your biggest cost- depreciation. Fuel, absolutely. Maintenance cost.....maybe. We bought our sedan at 265,000 with thorough maintenance records. Maintenance cost per mile since new is 8.1cpm. Prior to purchase 3.8cpm. During our ownership 20cpm. Part of this is due to a slightly bent rear axle that wasn't visible on purchase. Part was due to learning the hard way that you either find a TDI specialist or fix it yourself. Part of it is upgrading to more expensive parts like Bilstein struts. If I could do it again, I could have cut out a couple thousand dollars in expenses. As comparison my 94 F-350 has run 17.7cpm on maintenance over the last 100,000 miles that I've owned it.
Just realized you were asking if the rebuild was practical/economical. See above where unless the timing belt breaks this shouldn't even be a topic of discussion!
Spare Parts- When getting close to a timing belt interval, get the parts ordered so you will have them. You might consider keeping a set of filters. I run NAPA Gold/Wix oil/fuel filters but many stores don't stock them. I run VW air filters as I didn't like the fit of the NAPA/Wix filters for my application. Oil is the big thing as many TDIs have a very unique spec for the engine oil.....and it's not readily available in most parts of the country that aren't a big city on a coastline. Since my TDIs are older and less picky I run Rotella T 5W-40 synthetic. Same thing in the trucks so easier to stock 1 oil and any Wal Mart has it.
The A3, B4, and pre PD A4 engines are all pretty simple and straight forward. What you give up is horsepower and torque. The 2008 engines have more complex emissions and electronics. This is also what knocks the fuel mileage down on them. Someone else will have to comment on the PD engines. It would be very hard to find a A3 car that doesn't need a lot of work at this point. Unless you are willing to sink a lot of money in it or want to do it yourself, I'm not sure that would be the best choice.
I don't find the VAGCOM that hard to use. There are many great posts on here about how to do things with it. Owning one would most likely be a big help for troubleshooting in your area. It sounds like you may have worked on your vehicles over the years. TDI's just take some different tools and techniques than GM/Ford/Honda/Toyota. There will be a learning curve.
Good luck with your search.