40hp Lower unit removal

Last week I ran my 2003 40hp 4 stroke for the first time since last fall. It was ran in a barrel and I noticed the p-hole did not stream water. I bought an impeller and today I removed the 7 bolts (including the one under the anode) and tried to remove the lower unit. I didn't know how to disconnect the shift linkage and tried to remove the camnut and locknut. The camnut would only turn down so far and then it stopped. Then my son said the p-hole was clogged and sure enough it was. We never got the lower unit removed more than an inch due to the shift linkage and we just tried to put the camnut and locknut back to their original position then we bolted up the lower unti and tried it. Of course the water pump did work but now a new problem: it shifts fine into forward and neutral but it won't shift into reverse. I took the shift cable off and tried to put the level under the carb back by hand and it won't budge.
I believe somehow I got something back together incorrectly as I did not put the shifter into neutral and the gearcase probably wasn't either.
I need to know how to remove the shift linkage and get everything lined back up (and I still plan on installing the new impeller as a preventative measure). Does it disconnect up in fromt of the powerhead where it starts down into the shaft? or was I doing something wrong when I tried to disconnect it at the adjustment camnut?
Help!

[boats.net]

You need to remove lower unit, set lower unit and upper shift linkage in neutral then reassemble lower unit.

Thanks for the reply but now I think I've got bigger issues.
I took the lower unit off and put it on my workbench. I was able to get it into forward and neutral but not reverse. The shift linkage would only move up down one position. I put it and my shifter (I took the cable off and was shifting by hand next to the powerhead) into neutral. After I got the lower unit back in place I started the motor in a tub of water and it still doesn't go into reverse. When I tried to put it into reverse with the shifter by the powerhead it won't move further than neutral. Goes into forward fine. I took the magnetic nut off and I have metal shavings (not fine shavings but 10 to 30 thousands across).

I think my lower unit has a problem. I'm looking at my options, buy a new one (which units are compatable with the 2003 40hp 4 stroke?) or try and rebuild the old one. I can change out automobile gearcases so I think I can tackle this. Is this a clutch issue since it won't even shift into that position?
Any ideas?