A PI headswap is a better deal for the money unless there is some issue with your 98. While there is nothing inherently wrong with the pushrod 5.0, the overhead cam design makes more power for the displacement.
The downside to the overhead cam design is increased bulk and weight, but there is honestly more potential and the powerband is broader over the rpm range with an overhead cam 4.6 so the car you have is a better machine, strictly speaking.
Obviously you can build a pushrod engine into a screamer, but the 4.6 is better out of the box than the 5.0. You could sell your 98 and put the money into the 94 obviously, but there is a whole lot more to do, and things like clutch, brakes, shocks, bushings, etc. all have 4 more years of age on the older body. So unless there is something wrong with your 98, I would just do the PI swap on the 98 and enjoy your new high rpm power. It'll feel like a whole new car, and for far less money and downtime than the 94 would take to get to that point.