Re: lower end 1967 Mercury 39
I think those are all of the bolts for the LU. I have not worked on a 39 but I have the 75 and 110 of the same era and earlier and I do not remember any other nuts.
I think this was still in the years where Merc used carbon drive shafts (which really sucks). I could be that the drive shaft has rusted into the crank shaft or possibly the same scenario for the shift shaft (if it has one).
I have had limited success puttin the nut back on the front stud so it covers the threads and ginergly prying against the tower trying to push it down. This is dangerous b/c you can damage the tower or LU but it might help.
Do not try to fit a screw driver or pry bar btw the LU and tower--it will just break one or the other.
A final resort would be to try and pull the power head off. Take the nuts out and use a rubber mallet on the cylinder head to try and break the power head loose and lift out.