I'm swapping my guttles 3.9 for a 5.2 stroked to 390 with Speed master heads. swapping 42re to a 46rh. Running holley 650 spread bore. trying to eliminate as much electronics as possible, plan to use stock in tank fuel pump with bypass. Does anyone know of any problems I may encounter?

the main problem I am aware of is most of the carb intakes for the magnum motors are setup wrong.
the coolant bypass hose is straight on for the magnum motor, but the cheap intakes are at an angle off to the driver side, pretty far off from where the stock intake is.
and if you plan on keeping a/c from the factory motor, you will have spacer issues holding it up.
there is only one still in production that works and it is around 500 bucks.
if you swap it all the la accessories and the front of the motor, I think that solves the problem but then you have v belts to deal with.

I don't see an ignition system mentioned. And I presume you are intending on installing aftermarket gauges and speedo? If you intend to eliminate the ecm, you need to eliminate everything connected to it. That includes all the switches on or under the dash that uses the trucks buss bar resistance electronics.

You'll have to build a new gauge panel.
Bypass the abs isn't hard, but some line fabbing will be necessary.
There will be quite a bit of rewire to deal with all the stuff handled by modules, such as turn signals, power windows and so forth. You might be better off to get a painless kit
Everythings pretty much a bolt in though.

I went with a 5/8 bypass hose. I've gone with the magnum accessories fixture, lots of fab work but have generator, air compressor, steering pump, idler pulley and adjusting unit. And I'm on my third serpentine belt trying to get the right length. Only bad thing about that is I live about 30 miles from town. For ignition am running an old stock new Mallory distributor. Haven't gotten into all the electrical yet. Biggest problem I have is time. I'll be 81 next week and would like to finish this project soon enough to enjoy it for a while. I've learned that drag racing and street rods are a terminal illness. Once you catch it you can't get rid of it.

Rewiring your 03 truck will be a pain, but an aftermarket wiring harness, and eliminating the original harness may be the fastest and easiest way to solve a bunch of problems you are going to find. Splicing two completely different wire harnesses together can get complicated really quickly, go with one (OEM system) or the other (full aftermarket). There are several wiring "kits" out there that are good stuff at less expense then the above suggested name brand, Rebel Wiring comes to mind.

What you need to do is decide how many of those special features your 03 truck has that you just "need" to keep functioning and how may you can eliminate. The more back to the basics you go, the easier it will be to make everything work. Not very complicated to make it run, charge the battery, and run the headlights, tail lights, turn, and brake lights. A few simple accessories are not such a big deal t add, but every extra makes it more complicated.

Weedeater string works good here. If using the spring tensioner, look close, theres usually a safety range marking that is useful for targeting the belt length needed.

Simple and back to the basics is my goal. This is my fourth Dakota I've owned and the only problems I've ever had were electrical issues. This one is a SXT model, hand crank windows, manual door locks so not a lot of electrical. I got the serpentine belt problem fixed yesterday. Made the original belt off the 3.9 work by relocating the peg that locates the tensioner on the bracket. Right now I have the engine on stand to run and put some heat in it. Check for leaks etc. Started it a few weeks back but had no accessories. Now have everything to run it awhile. I believe it may be a little nastier than my original plan. Couldn't have much of a selection of cams. So bought a Hughes cam, roughly 565 lift, 236 duration, it should be a lot of fun.

Sounds like the Rebel basic 8 circuit wi9re harness is what might work well for you. It is a basic unit with 8 normal circuits, as long as you don't need a heater/ defroster power wire.
I found it at Rebel Wire Harness , part # RW100008 cost $258. Suppose to be USA made, but you know how that works these days.

You can but cheaper harnesses, but many of them don't have instructions and use really crappy connecters and stuff.