First: is this the standard dog clutch Cobra, or the cone clutch?
I looked around on the Crowley Marine website and found out the following:
If your model number starts with a 584, the 58=5.8 and the 4=4bbl carb, those models had the dog clutch.
If your model number starts with a 58FA or FB those had fuel injection and they had the cone clutch.
http://www.crowleymarine.com/1/OMC-Stern-Drive/1993.cfmIf it's the cone clutch I know nothing about those; but if it's the dog clutch model then read the following:
If you shift the drive manually with the shift rod it should lock into both fwd and rev, neutral is in the center.
When you changed the gear oil how much did you get in? Most Cobras take ~ 64 oz of gear oil, the ones for the 3.0 and 2.3 might take a bit less, but the regular V6/V8 gear cases take 64 oz or 2 qts.
The bottom most plug is the drain. The next one up next to the joint for the lower and upper gear cases is the fill plug. I pull out the dipstick in the top cover and remove both the drain and fill plugs. Then let it drain for a while. Next with new fiber washer gaskets replace the bottom most drain plug. Next set the dip stick in the hole in the top cover but do not tighten it yet. This allows air to escape so you can get all the fluid in. Now hook up the gear oil pump and slowly pump in fluid till the dipstick reads full. Then screw in the dipstick. Remove your pump from the fill hole and quickly install the fill plug. Last go up top and unscrew the dipstick and let it sit in the hole. This equalizes pressure in the drive and lets air out. Check it again and if it's a bit low you can add some through the top hole; tighten the dipstick.
That's the official OMC procedure right from the shop manual. When they are under filled it wipes out the upper gears first. You can see this if you remove the top cover.
You said you filled from the bottom; if you did that and didn't leave the next plug out till gear oil came out; and then filled it from there, it probably trapped an air bubble and was underfilled. Some people do it that way but that's not what OMC had in all their manuals
If you had water in the bellows you can get water in the gear oil but I doubt that would cause a major failure unless it was like that a long time.
http://www.crowleymarine.com/sterndrives/omc.htmlBTW Crowley Marine in Colorado sells rebuilt Cobra drives (dog clutch) but they aren't cheap....