Flex plate:
L26 or L32, the flex will be dual drilled for either a 245 or 258 converter. Shouldn't need to swap it.
Wiring:
Keep the 98 wiring harness and PCM. If it's an L26 there will be basically nothing different, because you'll tweak the emissions equipement to work on the new motor. If L32, you can take the map sensor connector and extend it a couple feet to reach the L32 map sensor. The L32 map sensor has the same connector as the L36/L26 motor. Personally I leave the wiring in the car so I don't have to fight the rear o2 sensor wiring. It's really a preference thing.

Throttle Body
L26 or L32 into a 98, you'll need a throttle body adapater from a Gen V to your TB that you'll be putting on. If it's an L32 Supercharged motor, I'd suggest the L67 throttle body be swapped in or a N*.
If you stick with a L36 or L67 throttle body, you won't have to do anything to the wiring for them. If you go N*/LS1 then you'll need a couple small wiring adapters for TPS/MAf or you can pull out the soldering gun and change those up with pigtails you can get at the JY.

Fuel rail:
You won't be able to use either the L26 or L32 fuel rail and injectors as they are for a returnless system and the car has a returning system. You'll want to swap over fuel rails based on which motor you have. NA get L36 rails/inj, SC get L67 setup.

Pulling/dropping in:
If you take the MC off the booster and flop it on the fender, you'll have a lot more room to put the engine/trans in together. An engine leveler is awesome in this area. drop the trans side to the floor and come in slow. you will level it out as it works it's way into the bay. I do these alone w/o issues. Same with pulling. Hell...last night I pulled a full drivetrain out of a 97. The booster was out and ...well I lifted it straight up due to the accident it had been in.

PS pump and AC:
Leave these in the car, do not disconnect the hoses. They bolt right up to the new motor. It'll take a second set of eyes to watch things, but you can easily manuver around these two. I do it alone as well. With a second person to help..it's cake.

Fuel lines:
If the car is being swapped from NA to SC, then consider the fuel lines. Many like braided lines with swagelock connectors etc. There's write ups and Tengis I think is selling a kit as well. If you are staying NA.. use existing fuel lines.

Engine mount:
The engine mount on either the L26 or L32 is on the oil pan instead of a stupid massive u shaped bracket. Looking at the bucket it sits in..there's a lip that sticks toward the motor. Take that lip off the subframe. The lip would hit the oil pan. There was a recent thread with pics.

Transmission:
If you are going to an 04+ trans. You'll either want to move the PNP switch to the new trans or repin the 20 pin connector for the pnp internal switch of the newer trans. Personally..I'd put the external on there. There is a thread on how to do it/line it up. If you are going to an L32, you need to change the passenger axle to one for that year. The HD trans comes with a larger differential and shorter passenger side axle than the L26/L32

Tuning:
If you are staying NA, then a tune should be done at some point. If you are changing over to SC'd, then a tune is definately required to run the engine. The injectors etc etc etc will be different.

If you need pics on anything ..I have a few hundred and can direct you to what you'd want to see.

Ask anything...there's at least 5 people that have done it.