Pulling the drive is not hard, they are heavy, though so I built a stand out of 2x6s to make it easier to R&R my old 88 Cobra. They weigh close to 100 lbs, so you do not want to be straining you back with this job. Now getting them back on can be harder, the stand really helped because it has adjustable casters underneath so I can set the height just right and don't have to worry about hefting it up and trying to keep the drive shaft lined up getting it back on. The alignment tool basically is aligning the engine to the gimble bearing, so that there is no strain on the splines in the engine coupler. The alignment should be checked when pulling the drive because if it's off, it can ruin the coupler and then you have to pull the motor to repalce the coupler. Sierra makes and aftermarket tool you can buy at local boat parts stores, I got one last year when I decided to try the R&R myself. You put grease on the very end of it and slide it through the gimble and look at the pattern of the splines on the grease, it should be even all the way around. Also the gimble bearing can swivel a little and the alignment tool gets the bearing in the proper position so the driveshaft will slide in, otherwise you can be fighting it for a long time. If you are going to do this get the tool. If the alignment is off, I'd take it to a pro to get it right, this can be hard for an I/O beginner. It can change because the engine mounts can settle a little over time.
You have a 98 Cobra SX so that is a joint venture (OMC/Volvo) product. I'd see if you can get a Volvo manual for the same year and take a look at it first. When I pull the drive I check inside the bellows for water. There will be grease in there from the gimble but there should be no water. Any water and you need a bellows. Not a terrible job but if you're an I/O beginner maybe better left to a good mechanic. Then I turn the gimble by hand and make sure it rotates smoothly. I grease it while turning it so the grease (Pennzoil Marine trailer wheel bearing grease) gets all thru the rollers. Then I check the u-joints for any loosness or binding, and grease them with the same stuff. I put OMC triple guard grease on the splines and check the seal around the drive shaft where it comes out of the upper unit. Finally I put some motor oil on the 2 orings on the driveshaft. Then I reinstall, the old style pure OMC Cobra does use a gasket, yours may not. I also clean out and lube up the shifter bellcrank in the pivot housing as these can get sticky and cause shifting problems. The first time I replaced the drive it took me about 1/2 hr to get it all lined up so it would slide on. It's a bit of a struggle, but doing the drive service and the tune up myself saves me over 500 every season. If I find a problem that is beyond me though, (leaking seal on the drive) I just take it to the mechanic.
Get the manual and read through and build a stand first if you have ANY back problems!
I put pix of my stand on the I/O forum over at
http://www.iboats.com that you can check out. Others have too.