You know supersize, I've thought about a lot of different engine swaps. You open up any 4x4 mag and there's a 4.3 in a Jeep, 4bt in a Scout, or a LS in some truggy. It's really tempting since we have pretty good salvage yards around in SD. It's just not the route I want to go. This is my first build, something I want to learn from, something I want to get done this Spring, and not get tangled in a harness for months on end.
It just feels like it's the best bet to stick with the 350, clean and machine, then overbore if necessary. Looks like its just going to come down to what is the best cam, head, and intake combo for me. So far there have been several good suggestions on where to look for heads. How do I pair the cam, head and intake? Just look for a package?
I hear and understand your reservations about the wiring and to be honest the hardest part about the wiring is ones self
There only these wires on mine..
-ground
-12 volt ign
-12 volt constant
-power to fuel pump
then a check engine light and diagnostic port, for me the light is right on the the plug bracket.
Some harness's are also already prewired for electric fan control too
My gauges are all mechanical
add some weld on bungs and 02 sensors
if you run a th-350 you need a 40.00 spacer for your crank, for the motor you can make adaptor plates for the engine mounts or buy them online for around 45.00..other wise trans bolts up no issues. The pass frame rail will need a little grinder love though with stock manifolds.
For the fuel system you can do a retrofit with a efi blazer tank with a tpi pump, or you can do an inline pump. I run a stock 98-02 40.00 vette fuel pressure/regulator and a 100.00 holly pump. his way I only have one line going to the motor, the return is right off the regulator on the frame rail

Russel makes an fittings to make this all stupid easy and its plug n play on the intake/fuel log.
The reward is drivability, reliability, a easier engine to service and work on, 1 piece rear main, higher amp alternator, serpentine belt set up, lighter/smaller higher tq starter, intake designed for torque, decent rpms "some take stock blocks to 6500 with tune", aluminum heads, very free flowing stock exhaust manifolds... oh and the whole 360hm/380tq starting numbers before a tune or a bit of work is not bad too

Id say with out a doubt it is a very easy conversion after you have a good reworked harness.
If you were to go with a bored 350 though I would find a good recommended package that others or a builder has had good success with.
Im not trying to pry at you, just I made the same reservations and once I finally did it I was amazed at how easy it actually was. i run a stock 6.0 with just a tune on my 07.. spins my 44's and has been happy living a life on the rev limiter non stop!