I have always went in and out from the top, and you don't have a lift, so that pretty much rules out coming out from the bottom anyway. The only time I find it easier to go in from the bottom is on a car with long-tube headers. As for tips,
1) Remove the cowl panel and wiper assembly. This will make it much easier to get to the top bell housing bolts, and will ensure that you don't break it when the engine is swinging around
2) The starter has 3 bolts, only one of which is easy to get to. Some people say to leave the top bolt out, but I don't recommend this. What I do recommend is don't take out that easy to see bolt until the other 2 are out. With that one still in there and tight, the starter itself won't fight you, and once the top 2 are loose, you should be able to reach your hand up there and get them out the rest of the way by hand.
3) Leave the wiring harness attached to the engine and just unplug the connectors at the back passenger side of the engine bay. It is much easier to transfer the wiring with both engines outside the car and next to each other than to try to remove every connector in the engine bay.
4) If you don't have it already, get the quick disconnect tool for the fuel and AC lines. Some people say to unbolt the AC compressor from the engine and leave it hanging to not have to re-charge the AC system, but any time I did that, I found it would always fall right in my way as I was pulling the engine out, and trying to drop the new one in, so now I just discharge the system, unhook the lines, and re-charge it when I am done.
5) While the engine is out, now is a good time to delete the ridiculous factory power steering line and replace it with a piece of braided stainless line. See instructions and part numbers here
This will also save you time because you don't have to waste time disconnecting the factory line at the pump, you can just cut it, and remove the rest of it and install the adapter fittings while the engine is out of the car.
6) With the engine out of the car, now is the time for some preventative maintenance. Even if they aren't leaking, replace the oil pan gasket, valve cover gaskets, oil filter adapter gasket, and front and rear main seals. Also if the intake manifold is all plastic, or even if it is getting old, replace it with one with an aluminum crossover. The lifespan on those intakes, whether all plastic or the ones with the aluminum crossover, is about 10 years, so if yours is original, or more than 6 or 7 years old, install a new one now while it is very easy to get to. Also go through the vacuum harness and make sure that any worn hoses are replaced while there is easy access.
Overall, pulling a 4.6 really isn't that difficult. My only other advice would be since you have a parts car, pull that engine first, this way if you break something, or forget a hose or a ground strap or something, you won't have to fix that too, and when pulling the one from your car, everything will be fresh in your memory.
-91 Cougar LS, coming soon, complete overhaul
with a 427" Windsor.
-90 XR7 5-speed black on black w/sunroof, MP2, coated rotors, double intercooler, 15%OD, ported heads, comp stage 1 cam, 85mm TB, 90MM LMAF, 80# injectors, and ported big valve heads
-98 Mark VIII LSC, Procharger P600b, TR3650 swap and 3.73s.
-90 SC Automatic rustbucket winter beater
-97 Tbird Sport 4.6 Nice weather daily driver
-"Your buddy Mike is INSANE!" -ClintD's dad