It sounds like you are serious about this and have some money to spend on it. I would recommend reading a bunch of build threads. You want to get a firm picture of what your end goal is. If you don't you will spend money on mods and then more money latter to upgrade them. Many people spend a lot of money on their first truck learning and then sell things at a loss to rebuild it. For example if you get duel stock cases now when you upgrade to 4.7 rear case you will want 23 spline and will have to buy a new coupler for your adapter. Little things like this add up quickly.

I totally agree!  My end goal would be to build it to be a pretty extreme crawler.  I am researching as much as I can and I am going to go with however the current setup is until I can get, and install, the parts I will want to have in there in the end.  For example, I will use the stock transfer case by itself until I can get dual cases with 4.7 (23 spline) in the back as you said, rather than dual stock and a future upgrade.

Right now the best investments you could make would be a welder and a torch or plasma cutter.

Are you reading my mind or what?  I was just discussing this exact topic with my wife at great length earlier today and she agrees that I need them badly since many upgrades and reinforcements are made with parts that are welded on.  The question is this: torch or plasma cutter?

As for the truck getting a dual case set up with 23 spline 4.7 in the rear would be safe upgrade as you will eventually do this anyway. It sounds like this is not a daily driver so weld the rear gears and get some used 31"-33" mud tires. This set up will take you 99% of the places you want to go.

I've heard of welding the gears but I'm not sure of which gears.  Would it be the gears in the differential so that they are permanently locked?  Is this the best option if I plan on only driving it off-road?

How many miles on the motor. Check the compression and valve clearance and carb. If you buy a new motor now you will regret it latter if you want more power and decide to do a motor swap.

I'm not sure how many miles are on the motor.  I know that my dad said that it was recently rebuilt but he doesn't think the carb was adjusted correctly and they put a bb in a vacuum line to get it to pass smog.  Also, it had a problem with overheating.  I'm thinking that I could rebuild it, but wouldn't it be better to get a 22RE?  One excellent reason for rebuilding it rather than getting the 22RE is because I already have it and it would be the cheapest route.  My question is this:  Am I going to be limited because of the carb?  Won't I run into problems when I reach extreme angles? 

As for bigger things like axles, gears, and lockers once you have decided what you want look for used axles already built. Toyota axles are not great for holding their value and if you wait for a deal you can get what you want used for half of what it would cost new.

That's the truth!  I found a W56 transmission for only $200.  Of course being new, I don't have any experience with how much this transmission should go for, but that seems like a really good deal to me.  As long as it is in good shape, I should be good to go in that department.  My dad also said that he has "heavy duty rear axles." I'm not too sure if they are made by Toyota or what.  I'm pretty sure that they are in an extra axle housing so at least there are a couple spare parts.

Anyways, here is what I know for sure:
1)  Although there is another heavier-duty, lower-geared transmission, I'm going to go with the W56 for now.  I may possibly want the R151F later, but my primary goal right now is to get rid of the L45.  The 4-speed just doesn't seem like it will cut it.  Besides, I think the W56 will do fine and I will only replace it if I have problems doing what I'll be doing with it.

2)  My tire size goal will be 37".  For now, I will put as big of a tire as I can get on the rims that are currently on it and go wheeling as much as I can with those.

3)  As I had stated earlier, I will use the stock transfer case and differentials by themselves until I can get dual cases with 4.7 (23 spline) in the back.  This will go to 5.29's in the differentials.  I am pretty confident in this setup based on what I've read.

4)  I am definitely going with the Hy-steer and crossover steering setup using the IFS steering box.  I don't see how I can really go with anything different in this department.  One quick question:  would I do well to find a 2WD truck at a junk yard and use the IFS steering box off of it or is it better to get the whole upgrade new?

The thing I am the most unsure of is the engine.  I'm not sure if I want to rebuild what I have, replace it with a 22RE, or prepare for something bigger (V6 or V8).  I love the track record of the 22R/RE so I'm leaning toward staying with it and then I could eventually build a buggy and then put a V8 in that.  If I do rebuild what is in it, I could stroke it and bore it out a little to add some more low-end torque which would no doubt be of some help.  Plus, I've rebuilt engines before and although they were airplane engines, I had a blast doing it!

I really appreciate the suggestions from everyone and I am sure that many pitfalls and wasted money will be avoided due to all your suggestions.