OK the standard alignment tool will work just fine on the Cobra, that's what I've been using for 10+ years.
Bellows, there are 2 ways to do it, one is to remove the exhaust bellows underneath it first (need a snap ring pliers to get the end of it off that fits into the pivot housing, other end has a hose clamp).Then by tiling the pivot housing, you can replace the D/S bellows leaving the pivot in place. I had heard of this method and asked my mechanics and they said it is better to do it the book way (remove the pivot housing) because you can better see that the end of the bellows that goes on the gimble housing really fit in correctly. So I did it that way. There are also 2 fiber washers between the pivot and the swivel houisng that may stay in place or fall out when you remvoe the bolts that hold the pivot housing on, I replaced those because they looked worn, and used some Evinrude triple guard grease to hold them in place when re-assembling. Also put OMC gasket sealer on the threads, that prevents corrosion and seizing.
Now normally you would disconnect the shift cable retainer when you do this, but then you have to re-adjust it afterward. So what I did was, disconnect the cable up on the engine bracket and rigged up a bungee cord to hold the pivot housing when I changed the bellows, this way I did not have to re-do the cable adjustment. On the Cobra, there are 2 special tools you need to accurately set up the transom cable, my method will save you having to get these tools. It is simple to disconnect the cable on the engine bracket, one end is just a cotter pin, the other is a trunnion held into the load lever with a cotter pin, I just put duct tape on the trunnion to keep it from turning (which would have changed the adjustment).
The Cobra bellows has a ridge on the inner lip that fits over the gimble flange, and there is a groove in the flange, that lip has to fit into the flange. I'll post up pix to make it more clear. The clamp for the DS bellows goes at about 1:00-2:00 o'clock position, this keeps it from chafing the bellows when you turn. The back end of the bellows just snaps into the pivot housing, no clamp there. I used OMC gasket sealer on the gimble flange to make a perfect seal. There are also a couple of ground straps that have a tab that has to go under the clamp on both the DS bellows and the exhaust bellows if I recall. And the slits on the bottom of the exhaust bellows are normal.
As far as parts, I'd use OE for both bellows, they are good quality and the first one installed on our boat lasted more than 10 years before small cracks appeared. Any Evinrude dealer can order parts for Cobras.
Before you reinstall the drive, make sure to clean out and grease the pocket in the pivot housing where the shift bell crank lives, water deposits can cause it to get stiff. I will oil the shaft with some motor oil which gets right in there and then pack the pocket with OMC triple guard grease which keeps out water.
When you reinstall the drive, get a can of OMC gasket sealer, or Merc perfect seal (Permatex Aviation also works) and coat both mating surfaces of the drive and pivot housing where the gasket fits and also coat that gasket on both sides. Also coat the threads of the six studs that hold the drive on. This will seal up that pocket and also make it easier to remove the drive next time.
