Ok, because this sounds exactly like me one year ago I'll give ya a synopsis of what I did. I had a 3.2 sitting around and eventually I wanted to build it up. I first took everything apart and cleaned it up really well, I sent the heads off to the machine shop to have the decks checked for true-ness, it turns out they had to deck them (run the mating surface of the head through a special mill to get it dead flat (within a half thousandth), I also had them throw my heads through the parts washer for a cool $10 a head and they came out like new! Nothing will motivate you to get cracking more than shiny parts! Anywho I made sure to clean my valves using a brass wheel on a grinder, that got them to pretty much new condition. I then hand lapped the valves, because I could tell that they were not sealing very well (you can do this yourself for $10 and some time, or you can have a machine shop grind them to the exact spec, but honestly I think it's worth just taking your time and doing it the old fashioned way). After cleaning up all of the valve components I then ported and polished the heads, the gains from such a modification are disputed, but I thought "why the **** not" and spent many nights getting each port perfect and I'm happy I did. I also invested in some 3.0 cams, many people dispute the effectiveness of this upgrade, but I figured while I'm in their it's a pretty cheap modification, especially if you already have the cams. After assembling the heads I then turned to the shortblock. The very first thing I did after cleaning up the block is bought some micrometers and telescoping gauges to measure all of the specs on the block. While tedious and in 90% of cases unnecessary I didn't know the history of the engine I was working with and I would be ****** if I found out there was an issue that came up, just because I didn't spend some time and about $40 at Harbor freight on some measuring tools to fix the problem to begin with. My vote is to just blueprint the block. If nothing else you gain skill from such an exercise. I personally went with DNJ gaskets, because I'm a broke college kid, but I mad damn sure to get myself some Ford cam seals for a premium price, because I've heard many horror stories about those failing. If you have the money go with either OEM or fel-pro as I have yet to hear any sketchy stories about those brands, you may also want to snag some new head bolts as it's generally a good practice as they do stretch in tension. I went with some DNJ piston rings (I had to buy 2 sets because I snapped a ring on installation so if you snap one, you know who to call

) and filed them to within a thousandth of each other. Whether or not this extra effort to get them all perfect makes a huge difference is beyond me, but the way I see it, there shouldn't be a power imbalance, between cylinders. You certainly could go with Hastings, once again it came down to price for me. Rod bearings: Replace them. Main bearings: take a good look at them and ensure they are within spec via some elcheap-o plastiguage. The mains are a pain in the ass to replace as they are SUPER rare to be found in the STD spec, so you would need to go to a machine shop and things can get sketchy when you put any part from the bottom end of a SHO motor on a mill. This would be a great time to paint the block, intake, valve covers, ect, ect, and also a great time to yank out those rusty freeze plugs!
There is a lot of little steps to complete your goal, but so long as you have a good source and the determination you can do it.
Some good sources:
Shoforum
shoforum
https://www.facebook.com/tucker.grimley/media_set?set=a.1954062067885.55429.1732680692&type=3 I have documented a whole rebuild here^
http://www.youtube.com/user/Jafromobile this man knows his stuff
Factory service manual (the spec sheet is the most important thing you will read in your entire life, or at LEAST get a chiltons)
Automotive engine rebuilding, second edition (if you really want to take your time)
http://www.youtube.com/user/VeryTucker I have a few SHO how to vids
https://www.facebook.com/groups/2254469276/ the SHO owners club group
Google (the least useful of these sources)
The best thing you can do is take your time, don't rush to get things done! Double check your work, and above all act like a craftsman. The best way to do top quality work by yourself is to take great pride in your work.
If you have any questions fell free to shoot me a PM
-Waffles