It is a lot of work, but the results in my opinion, are worth it. But, it was my first engine swap, so I may have felt a bigger sense of accomplishment then someone who has done it enough to despise that sort of work. The car being very sentimental to me also made it all that much more special - sounds odd but in short it's one of those connections I have left to my father who past away three years ago (originally was his car).
Once you remove the air boxes, intake plenum, and start removing hoses and disconnecting the wiring (PCM and battery cables), it's all grunt work from there on out. Four mount bolts, twelve support collar bolts, and if I recall correctly six-eight bolts for the bell-housing/starter. Then you can hear the greatest sound ever, the engine being lifted out!
My words of advice, take a powered tool that can remove bolts with ease, those new battery impact drills are freaking gods gift to us. Bring a hack-saw, as you're going to have to cut some hoses, as much as you're likely going to hate to. Also every assortment of hex, torqx and socket sizes from 7-22 mm (deep AND shallow), hell even a wrench set for those transmission bolts.
I forgot to mention one thing I do to check an engine is look into the oil fill cap as generally you can see down into the heads internals. Not so much a feasible trick on the 3.5 unfortunately. Pop the valve covers off and if your able to the oil pan. Surely from there you can tell everything. If you haven't found any metal shavings, sludge or any other scary looking components you may just be OK. If you also drain the oil, look for milky-shake color residue in the oil, a clear sign of Preston in the oil which could indicate a gasket issue somewhere.
Pull that upper timing belt cover off on the driver side of the motor and make sure the belt is tight first and foremost. If it isn't, well decide if you should pull the rest of the cover off to see if it's just come loose from sitting or broke, either scenario a loose or broke belt means damaged valves.
Kinda jumping all over the place but I'm just spewing out everything that comes to mind as I think about when I was doing the project myself. LOL!
I prepared my motor to be dropped which was remove everything I wanted maintained (hoses, wires, etc). My friends yard just cuts everything. They raised the car on a fork life, took a torch to the cradle pushings and I watched it drop to the ground, and dangle by the struts. Than they removed the car away and stripped everything away from the motor (cradle, tranny etc).