I personally like the 1st gens - 1997 to 2002s. They're built like a truck and feel like a tuck because they are. Basically an enclosed F-150. From being on the forums, here's what I can tell you about the early vehicles:

Spark plug issue is due, in my opinion overall, to wrongful installation and use of other spark plugs besides the Motorcraft brand. They are aluminum heads so they don't need to be torqued real tight like we generally do on cast iron heads.

1999 had the head issue where it was milled wrongly and caused an oil leak...don't know how big of problem that was. Additionally, I believe 99 was the first year Ford did away with the 2H option and went to AWD - 4H - 4L on 4WD equipped vehicles. Not a problem per say, just a side note...

Also, IIRC, after 99, 5.4L got equipped with the Super Duty transmission behind it.

Avoid Expys with the air ride suspension. A lot of people have problems with the air bags leaking and it's just expensive to repair. If you do though, you can replace them with standard springs like the other models had and you are good.

I wouldn't go with the 4.6L either. People say it's doggy and I believe them. You will happier in the long run with the 5.4L. It's a heavy vehicle and the extra power is nice to have on tap. Also, I'd personally avoid the Expys with the smaller 8.8" rear end (very easy to distinguish between the two). If you need to tow anything, you know you have a bigger and sturdier rear end that can do it. Just my opinion though...

If you find one, check all the doors for rust on the at the bottom on the inside. It's a common area for rust to develop due to drainage problems. However, there is nothing that cannot be fixed.

Honestly, I love the way mine is equipped and I'd recommend doing the same:
I have a 97 with the 5.4L, 4WD, 9.75" rear end w/ 3.73 limited slip. Cloth interior, rear A/C, etc. It's an XLT model. Came with factory tow package and has all the external oil coolers, etc - although you can add those yourself.

If you find one, there are decoders for the VIN and door tag here that will tell you EXACTLY what the truck is equipped with.