I'd agree with others' advice to replace the heater hoses. General rule I'm guessing we all try and follow is "I've gotten this far...might as well while I'm here."
You do have to change the steel heater line under the manifold. the original non-PI one will not work as the PI intake's runners are deeper and will hit the tube. If you have a knock/sound insulator for the PI intake, you'll see that it has a relief molded into the left side to fit the PI heater tube.
If you're replacing the heater nipple behind the water pump, use care as I've heard stories of folks smashing it too hard and breaking the block. If not, I'd suggest the correct o-rings and a liberal amount of sealant.
My practice, now that I've done this job more than a couple times, is to remove the wiper/cowl assembly. It can be done without removing it but for me it just makes everything easier and more accessible, especially the left side crash bracket and the bolt holding it in the back of the block.
I've found that the 20 to 40 minutes added taking that wiper cowl off and putting it back on will save at least an hour to an hour and a half when putting everything together. Plus it makes it so much easier to get to the 4 and 8 plugs if your gonna change them while your at it.
Again good luck
2005 Lincoln Town Car Signature Limited
5.4 liter throttle body; PI oil cooler, intake tube & air box; Mark VIII aluminum driveshaft; Trac-Lok limited slip; Richmond Gear axle shafts; J-Mod with Sonnax valves; Limo rear control arms and a great sounding stereo that won't ever automatically remember my Bluetooth settings
1999 Mercury Grand Marquis (gave that to youngest son, and he's now a converted true believer)