Ok, from what you have said both trucks will need the KDP addressed, so that's a wash either way.
I think the 12 valve may be a little cheaper to turn up, but HP per HP you will have to deal with more EGTs with the 12 vlave than with the 24 valve, so the overall cost to get "useable" HP will probably be about the same either way.
I'd have to say that the $$ you'll spend on BOMBS is more likely to be tied to how far you want to go than to which truck you have.
The P7100 pump on the '94 should be more durable than the early VP-44 on the 98 (a definate pro for the 94). There were some known issues with the early VP-44s failing when fueling boxes were added.
If memory serves me the '94 will have 175hp and the '98 will have 215. From my experience with the stock 175 hp truck it will be a dog. You'll want a plate of some kind (about $250) and governor springs (about $175) at the least. BTW, a #4 plate will make that 94 go like a bat-out-of-h.

You'll be right at the limit of what the stock clutch will hold though and you will be able to get into EGT troubles if you push it hard enough.
On the 98 you can do a low-end box like the EZ along with some injectors like DDII's and it'll pull hard enough to need a clutch. I think the box is about $500 and the injectors will be the same.
The price seems fair on the '94, I gave that much for the truck in my sig (it was stock then too) with 83k on it and it needed brakes and ball joints, but it is a club cab.
I hope this helps your decision.
Mike