IMO this could end up being a train wreck. Some of it from poor planing. Some from bad advice.
From looking over this thread it's clear there's a misunderstanding about what should kept and what to swap when performing a motor swap.
IF putting a 98 V8 into a 99 GT, this is a straight forward swap. It's a silly swap but it will work without a ton of re-working as it's basically a Windsor to Romeo swap.
Why is this a silly swap? Because it's very easy to find low mileage PI Romeo's from wrecked 2001+ Town Car, Grand Marquis, Crown Vic. I paid $800 for a 35k mile 4.6 from a 2003 Grand Marquis. It doesn't seem to me that $500 for a motor that really isn't a good fit is a "steal".
IF putting a 98 V8 into a 99 V6 car, this is anything but a straight forward swap. All I can say is, bumpy road ahead. Good luck.
For everything that follows I'm going to assume that the swap is a 98 V8 into a 99 GT:
In a modern car, the electronics are king. If you are looking for a straight forward swap, the goal should be to retain as much of the original car's external systems as possible.
The talk about needing to change the fuel system is wrong. The fuel system is basically an external support system to the motor. That includes the wiring, induction, exhaust.
Note, I have done a Windsor to Romeo motor swap. So I'm speaking from direct experience. What I did was put both motors on engine stands and make the new motor look like the old. When this is done there are only minor differences between the motors which are solvable (PVC, heater hose, temperature sensors, flywheel, front belt routing, ignition, ect). There are tons of threads on how to do a Windsor to Romeo swap.
Should this really be a V6 to V8 swap, there are tons of threads on this swap as well. These are not as likely to be encouraging. Should this be the case, allow me to apologize for adding un-needed information to your thread.