Well, changing out the clutch that you know is bad is probably a pretty good thing - going through the trouble of changing the transmission (Except you won't have to :thumbsup) and guessing whether your old clutch is reusable or not be nervewracking - and usually you just should.
Hopefully your Dad can help you out finding good quality parts at a reasonable price. In any case, you are going to have to get the transmission (and T-case) out of the way to replace the clutch parts (probably part of the exhaust as well) and then line up and put everything lined up and put back together after the clutch parts are in (clutch kits usually have a plastic thingy in there to help get your clutch spinning parts lined up). Haven't worked with 4WD setups myself - but lots of people on this forum/in this thread who can probably do it in their sleep. With some time, and space to work, and some advice-seeking,/reading up you should be fine.
Something to consider is that you probably want to replace the internal slave cylinder while you are in there, which will probably mean you want to replace the master cylinder (on the clutch pedal) so you don't ruin the new slave and end up doing this all over again. There is an itty-bitty $10 ford tool to disconnect the clutch hydraulic line that you will want to source online (ebay, amazon etc) or make arrangements to borrow. Also read up on pre-bleeding the clutch master/bleeding the clutch ystem after installation.
Maybe you see more rust damage than is visible in the photos, but looks like this BII is VERY worth saving for the price of a new clutch!
Afterthought: no disrespect intended towards your father. I merely meant, that, usually when you buy a vehicle off a stranger, there is is some question into what they think is right and wrong with their vehicle. In some cases it's not knowing, in others its a rosy bit of self-deception, which we all can be guilty of. In this case, it's all good - your father knows vehicles, knows THIS vehicle, and is not going to steer you wrong about it. Before getting knuckles deep in this, you might see if he has any advice is all...