It will be a fairly straight forward swap if you re-use your stock 98 PCM and have EFILIVE to tune it. The stock MEFI-4 controller won't fair to well in marine tuning for the street, but I have heard of some doing the 0411 PCM swap from an 01 van to the marine engines and GM performance engines that used MEFI-4 or MEFI-5 fuel injection. You'll want to swap the camshaft as the stock marine cam will perform like crap above about 4400(but realistically starts dieing off around 4000-4200). Check over at EFILIVE.com for the 0411 PCM swap and also look up on fullsizechevy.com for the marine intake swap. This is a popular swap on the 350's as the stock CSFI that GM used sucks to say the least in slightly modded form, and is marginal even stock. GM still today produces the old tried and true L31 5.7L engine like was used in 1500/2500's from 96-98 and 3500's up until 00. The only LS based engine they use in marine is the 6.0L as the aluminum heads of the 5.3L worry many in the marine industry for electrolisis and corrsion. I believe also you can get software to tune the MEFI fuel injection from MSD and ARIZONA SPEED if you want to go that route.
I know a bit about the marine engines, so if you have any specific questions ask away and I'll try and answer them.