I want to say yes, but I don't know the manual transmission setups very well. I know the automatics have balance weights on the flex plate, and a different harmonic balancer than the 5.2 motors do.
If you balance the 360 when you build it, then you can use any flywheel and harmonic balancer you want.
Although, you should be able to buy a Dakota flywheel from a 98 right up to 03, if I remember right.
OBD2 is the way to go. There are way more options for tuning it. If you start upgrading past a basic cam swap, the OBD 1 isn't going to play as nicely with it as you'd like.
Understandable.
The people who rave about him are the ones who don't know any better. I had fuel puking out of my exhaust when I had my stroker motor in my Dakota.
That went away when I bought the Dart and swapped the Magnum 390 over to a carb. LOL!
B&G would be my first choice for having a tune done. I used them for tuning my wild nitrous fed 318, and Dave did a great job with it.
They don't come cheap, though.
You can get a nice custom grind that will be EFI friendly. I use Comp Cams for my stuff, but almost any good manufacturer will be able to make something to suit your needs.
How are you planning on tuning it?