As MDA8569 stated, there is hardly any differences between the 5.2 and 5.9s. If I recall correctly, the 5.9s are only bored out a bit more.
Converting to OBDII is a difficult task as you are basically replacing the entire control system with a newer version. If you are only planning on keeping the truck for 5 years, don't bother, it's a waste of time and money. But, if you are like some of us on here who plan on keeping out trucks up and running for the next 5-10+ years, go for it, you will thank yourself in the long run.
As far as resale value goes, these are going on 20 year old trucks, it doesn't matter if you invent and install OBDIII, its not going to raise the value by more than a can of beans to anyone except you. If I was buying and really wanted an OBDII truck, i'd buy one from the applicable years, not convert or buy one that was converted. However, if I already had one that was OBDI, i'd convert it, because I plan on driving my truck for a long time.
A Mopar PCM (if you dont want to convert) is one of the easiest ways to get more performance from your truck. Followed by heads, cams, intake and headers.
As for putting parts on that are worth more than the truck. Anyone who has spent more than about $2500-3000 worth of work on their truck has put in as much as its worth. I'll be honest, anyone who says these trucks at their age are worth more than that, is kidding themselves in the standard market. You will not find a person who is on a dealer lot looking at trucks who will compare a 2016 Silverado for $20k with our trucks at anything above $1500. Its just not going to happen. To us though, our trucks are nearly worth their weight in gold. I wouldn't sell my hunk of junk for anything less than $8k, which is why I will never sell it, because no one will pay.
My point is, if you truly care for your truck, you won't be bothered by spending time and money on it. But if $3k sounds like its too much money to spend on the thing for upgrades over the years, look for something newer, you'll be happier in the long run.