Very do-able project for the home mechanic. Been done by tons of ppl (including myself). Another option is to use a motor from a 2000+ Crown Vic, Grand Marquis, or town car.
Check out car-part.com for a searchable list of salvage yards in your area.
There are tons of posts from others that have done this and similar swaps.
There are so many threads about this swap that it's almost impossible not to find one.
In a nut shell, re-use the wiring, ignition, fuel injectors from the original motor. Depending on the donor motor determines what else will need to be transplated.
The original PCM will run the PI motor and it does not have to be tuned. Of course, it will run better with a tune.
The 98 has two temperature sensors on the intake cross over where as the 99+'s have only one. There are multiple ways to solve this problem depending upon your preference.
One method is to drill and tap the cross over for the 2nd sensor. Another method is to use a block drain plug near a freeze plug. This involves making a simple harness extension.
The valley heater return line is different. Either get a hard line from a 99+ or swap the water pump nipple.
Depending upon the MY of the donor motor, there could be slight differences in the PCV system. Nothing that is too difficult to over come.
If the original has an oil level sensor and you wish to retain this feature, then it will be necessary to swap oil pans.
It may be necessary to swap flex plates or flywheels depending upon your transmission type and the transmission type of the donor. Again, very straight forward as all modular motors use neutral balanced flexplate/flywheels. Obviously you have to match the crank bolt pattern (6/8 bolts).