I have an 03 magnum trans and an 02 mag motor in my 98.
I don't think it was hard, but then again I've done a decent amout to my car.

The magnum engine was put in 01 and up R/Ts and ACRs. The first gen wiring harness works on every sensor minus the coolant temp sensor (you need to swap your first gen one on) and the cam sensor is the updated one. My 1998 has the updated one, but ones pre 1998 might not. Easy, swap your old cam sensor on if you can't use the old one.
You can reuse your old first gen intake manifold, or with some hacking make the magnum intake manifold on. You need to move the radiator forward (mod the brackets) and trim the fan(s) so they don't rub against the intake manifold. To use a 2nd gen throttle body, one from a 00 is prefered since you can use your first gen idle air senser. You may need to extend the map sensor wires because the map on the magnum intake manifold is all the way on the left. You will need to make your own air intake reguardless. If you use an 01-up throttle body, you can set the idle by cracking open the throttle body butterfly with the idle set screw. Strap the old idle air controller aside and leave it plugged in so it won't set off a code. In either case, you have to use the 2nd gen throttle body cable bracket because the first gen bracket on the second gen throttle body opens the butterfly past open. Not good.
to control the butterflies in the intake manifold, you can either rig up an rpm switch (harlan is the cheapest way) or wire it up to a switch inside the cabin to turn them on whenever you want. The prefered range to have them on is 4.9k rpm to redline.
You have to swap the outer timing belt cover and pass side mount on the engine from your old sohc.
As for the exhaust side of things, a regular exhaust manifold gasket will obstruct the magnum's ports (mag ports are 4mm or so bigger than the gasket) and a factory mls magnum exhaust gasket is too big for use with the factory exhaust manifold (it won't seal). What I have seen is a victor reinz? gasket that looks like it may work. But I'm not sure. Currently I'm using the factory magnum exhaust manifold and cat, which line up perfectly on a first gen neon. The upstream o2 plugs right in no problem, but the downstream o2 is located in the catalytic converter on the driver's side. I took the downstream o2 plug/wires out of the plastic ties holding them down and ran them under the cat to the driver's side of the cat where the 02 bung is. The second gen exhaust is different after it goes around the gas tank so I believe it will not fit on a first gen.
All the other sensors plug in/work fine.
You need to swap over the crank pulley as well. Great time to do a UDP. May need to swap your old power steering/ac on, I wouldn't know, I have neither.
As for the trans you have some work cut out for you.
You need to use the bellhousing of a first gen (or 00) because 01+ neons use a hydrolic setup, not cable.
You need to seperate the bellhousings from both trans, clean the surfaces of the first gen bell housing and the second gen trans (I used alcohol pads), and seal them with anerobic sealant (this stuff is like $14!). You can get the mopar stuff from the dealer, but permatex does make it too. This is a special sealer that only forms it's gasket when pressure is applied. It is the only stuff you can/should use. You may need to shim the diff. It's part of the proper thing to do. Luckily, mine is fine, and I don't even know how to shim it.

It can be a little bit of a pita trying to line up the bellhousings. Looking back, I would have taken it to someone who could have done it properly. Now is a great time to install an lsd and/or diff safing tabs to hopefully keep the diff pin in (unless you put in a quaiffe)
I would install new axle seals as a precausion (they pop in/out) and it's easy as pie. Now is also a great time if you plan on doing header/brakes/struts/springs/bushings/clutch/what have you.
You can of course just bolt on your old tranny.
I highly suggest the 3.94 geared trans over the 3.55. With the magnum tranny your revs will be a bit high on the freeway though.
Also, transfer all your old engine mounts.
I'm pretty sleepy now, but if any more questions ask away!