if you have low spots from sanding the shell, determine how low and how many their are. if its not too bad, the glue will sorta fill the low spots.
if you try to fill those spots with something, you will have to sand the shell again to make it all smooth. that in turn may cause low spots in the areas you didn't need filler in. just be careful.
as for covering the holes on the inside (when gluing) go for it with painters tape. its just glue, so when you go to drill the original holes again (using the proper size of bit as not to enlarge them bigger) it will clean out the excess glue too.
it would be a good idea to paper and tape the inside and edges before you start gluing (see edges remark below) you will have glue on your hands and you don't wanna transfer it to the inside of the shell.
once the shell is ready to veneer, cut to size and dry fit the veener so there's no issues when its time to glue. i usually cut it about 1/2 to 1 inch longer for the over lap and about 1/4 over the depth of the shell (or whatever you prefer) this gives you play in case it walks on you. but you are doing it by hand, so you shouldn't have that problem.
locate were you wanna put the seam and use a straight edge to draw a line down the shell. this will be your starting point. make sure the straight end of the veneer goes down first.there's no overlap like wrap material so it doesn't matter which way you roll.
when rolling the veneer to the shell, make sure its nice and tight. with veneer it will show gaps more than wrap and prone to bubbling later on.ALSO make sure you have a clean surface that your rolling on. if there's a tiny bit of dry glue or tiny scrap wood on the table, it will break the veneer. remember,it real thin.
i was taught to roll the glue on the shell twice. once on the shell, move to the veneer/wrap, back to the shell (once its little tacky) then back to the venner. you don't have to go thick when rolling.its just going to take longer to dry. just make sure its even.it also depends on the weather. if its real hot the glue will set faster.
from here i would sand and seal the outside before i drill the holes out. that way you don't get over spray in the holes again.when the shell and veneer are dry, you will need to feather in the edges by sanding were it meets the venner depending how you did it. i would say do this before you seal it.
as for the edges, i would have to see it...but if your going to recut them then you can get away with cutting the excess veneer off with a knife. if you wanna save the edges, then just be careful when trimming. this way the veneer goes to the edges and it looks cleaner.
as for triming the seam, once you come around to the seam when gluing, have a sharp blade and line up your straight edge with the edges of the UNDER seam. so when you cut the top veneer it should butt up perfectly. again,that's why you need a straight edge underneath to begin with.you might need to use a small roller to press the seam together and make it flush.
i don't know what to use to seal the veneer as i never did it at home-just work. i'm sure someone else knows the answer here.
lay the shell on the face on a hard surface and use a center punch thru the inside to mark a dimple on the outside so you know were to drill. try to center the punch head in the holes. in some cases you can see it, but when you drill the bit will usually fall in line with the original holes.
then takle cleaning the parts. i have a bag of lug screws if you don't wanna clean them. unless they don't need to be cleaned.