'88 Diesel Jimmy in trouble

Hi, I have a '88 6.2 diesel Jimmy sierra classic. It's old, lots of miles, and seems to have the tranny clunking when I put it in reverse, drive, and when its shifting gears. Also, I want my 2yr old to inherite it when he's 16. What's the best way to keep this awesome truck in good condition? My wife and I are on a very strict budget (We have two boys, ages 7m and 2 yrs, and only one income), and it's our only vehicle, so it's run daily with me going to work, dr's apts, and grocery runs. Is it possible for me to be able to rebuild the tranny on my own (I don't have allot of experience on diesels), or would it just be best all around if I bought a rebuilt one. Also, is it really good to do fuel injecter cleaner in the fuel tank at every other filling? Or is the guy at the parts store just want my money?
Thanks for the help you can offer.
Chris K  

Being diesel has nothing to do with that transmission.

Is it auto or manual?

Guy at the auto parts store wants your money, don't bother with injector cleaner.  
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Auto. I inherited it from my Uncle in '06, we sold it in '08, and when we saw the person we sold it to, we found that they were running it into the ground. No tune up at all for an entire year, fried one of the batteries, and didn't replace it, the list goes on and on. Since we got it back we've replaced both batteries, glow plugs, oil change, tires, and batterie cables. It's running better, but still feels like theres something not working right. Our next step is replacing the air filter, and then we're thinking on taking it to an actual machanic. Not a shop, but a friend of ours who's a machanic. When Tax return hits we have to check out the wires in the dash. Heater doesn't always work because the switch doesn't always connect, and the speakers for the sterio have disconnected, so we have to work on that too. Here in Juneau it's get's pretty chilly, and we have to have a warm vehicle for our little boys.
Thanks for the info.