1- Will a '99 bravo 3 upper bolt to a '05 lower?
2- Can the upper gears, clutch cone, from the 99 go into the upper 05 case or have the drives changed between years?

Im pretty sure that they can bolt up. I am not to sure about the gear swap. Contact Merc. probably going to have to shim and set some lash.

idon't think you can bolt them togethereI believe you will have a huge oilleak between the two case halves...ther is tot he best of my knowledge a service bulletin that tells which cases will work to gether and which ones won't, be advised they wil all bolt together just the newer ones have an extra oil passae in them

Carm,
The cases should match up, but you need to check for the oil passage on the old and the new upper. Looking at the lower unit, from the top, in front of the vertical shaft is a large water passage. On the side closest to the vert shaft there is a bump that will have a small hole in it. There is also a quad seal in and indentation. If you have that, the upper should be a go.
You can NOT just put the 99 gears in the 05 case unless your 99 serial number begins with OM, or it has been upgraded to the newer X gears. I suspect that it isnt or hasnt been.. so a new gear set kit is needed.
If you have more questions.. feel free to give me a call .. 616-403-1006.

Hope this helps.
D*ck

Thanks for the responses guys.
Mr. G, you helped me out the beginning of the season with my xr, clutch cone problem. Your advice is always wecome, as is everyone elses, especially offering your phone #. I used it last time, hopefully I won't need to bother you again.
Thanks all!