I'm confused. You said, "... I went thru the tedious finishing process of sanding, epoxing and staining. I recently completed my my last coats of stain........"  

1.  What were you staining after epoxy was already installed? 

2. Did I understand right that you started the boat in class in 2011 and just now finished it in 2014?  

3. Where was it for three years? Was there epoxy on both sides of the wood? 

4. Did I understand that you have a basket ball sized area where the glass and epoxy is pulled away(delaminated)  from the wood core? 

   5. if you stained the wood then glassed and epoxied was the stain compatable with the epoxy? 

some pics might be useful.

also, did it bubble after exposure to heat?

   Sorry for the confusion, I sandied in between the epoxy coats and than   applied about 3/4 coats of the Schooner Poly Marine varnish (not varnish) on  the inside and the rails as advised by CLC to help with UV protection. Yes, I went to boat school in  2011, I lost a year building a garage and I worked on it sparingly for a while. I recently moved and now have a  real wood/boat shop  where I have been attempting to finish the project. Both sides were glassed and epoxied when I took the class, I have applied 3/4 additional coats of epoxy when this project started to unravell.I should also state that the boat was covered and inside a garage when I wasn't working on it so it never was exposed to extreme weather conditions. In response to the size of the bubbles, I have a few patches the size of a baseball. I spoke with CLC yesterday and was advised to just address the bubbles insterad of sanding everything down to wood and starting over. The bubbles started to appear after being out in the sunlight,

   I would address the bubbles too. Whether I'd cut each out sand and patch that area or inject epoxy behind the bubble would depend upon the size, placement and squishyness of the bubble.  For the most part I'd probably sand and patch outdoors in the sun so I could see them easier. Then leave the boat out there so the skin would heat up, show others and/or dry out the bubble area.

I've never experienced this on a new hull. Some older hulls did this after some use, abuse and water intrusion through damage. 

>>>>After about an hour I discovered to have about 10 different sizes of bubbles all over the boat, they arranged in size of a quarter to the size  of a baseball. >>>>

99% of the time* this is an epoxy mix issue.  Specifically, the first layer of fiberglass (presumably on the inside of the boat), was wetted-out with epoxy that was either insufficiently mixed in the cup, or not mixed at all.

This happens.  We've all done it.  The epoxy doesn't change color or in any other way signal that it's properly mixed or not.  So if your mind wanders it's easy to just walk right over to the boat and dump the cup of barely-mingled resin and hardener in the boat and start wetting out the fiberglass.  

SOME mixing occurs, just in the process of pumping from the classroom bulk dispensers into the cup, and spreading it on the fiberglass, so the epoxy achieves a sort of superficial cure.  That must be what happened here.  Otherwise, you and the instructor would have caught it the next day when everyone's epoxy was cured but yours was sticky.  

This scenario generally presents as a sort of patchwork failure.  Some areas got mixed enough to cure, while other areas are all resin or all hardener.  That's why you see patchy failure, rather than the entire sheet of fiberglass peeling off.

Why did this not show up until now?  Well, the boat was in your shop, out of the sun.  The last time it was in the sun for any length of time, it was upside down on your car on the way home from the class.  So the big day comes and the boat is rolled out into the sunshine for a day or two. The surface temps get up to 100F or more. Deep beneath layers of properly activated epoxy, which are concealing the bad first layer, you have fiberglass that in some areas is moistened with unmixed resin and hardener and not actually bonded to the plywood.

The unactivated patches of resin and hardener, still more liquid than plastic, expand in the prolonged heat of the sun and create the bubbles you're seeing.  

There's no fix for it but to excise the bad patches with a razor and fill those spots.  

Again, this happens to everyone, at least if you do much epoxy work.  I've done it, oh, more times than I care to admit.  Heck, every professional boatbuilder knows of some 40-foot pre-preg or vacuum-infused racing boat hull that didn't kick off for some reason and ends up a much worse mess than this. (An infamous such disaster here in Annapolis ended with the ruined racing yacht hull buried to the deck in someone's back yard and turned into a swimming pool.)

So don't feel bad, and take heart that it was probably just one bad batch, probably handed to you by a classmate.  (That's usually how this happens.)  There'll be some messy clean-up and repair, then all is forgotten and you're on your way.  

For everyone reading this who's biting their nails...good!  Don't forget to mix your epoxy!

*The other 1% of the time it's a surface contamination issue, say, using an oil-based stain under the fiberglass.  But this is unlikely-to-impossible in a classroom setting.  

so with respect to fixing this kind of thing....i recently went through a similar episode.  here is the approach i used....and it has been fine and you cannot see the repair if done properly:

i first tested the boat to identify all the problem areas.  there are the obvious problems (the bubbles that you see) and the less obvious ones which are where the epoxy is not fully cured but has not bubbled yet.  for the less obvious kind, i tested the entire hull probing it with my thumb nail.  if i could not dent it, it was fully cured, if i could make a dent....this is partially cured epoxy.

 i then lightly scored the perimeter of the each problem spot with a razor so it was easy to see. a heat gun was used to apply heat to the soft epoxy and with a razor and razor scraper i pulled the epoxy/glass off in these spots.

i then used 80 grit sandpaper on a ROS sander to clean it up and to sand along the cut edge to cut back into solid epoxy (no heat involved).  if you are working with okoume, you will probably want to clean it up with a sanding block and lighter paper (i had the problem on a strip built boat) to avoid cutting through your veneer.  the 'advantage' (if you can call anything an advantage in this annoying episode) of this technique is that you can really discover where the edge between cured and not fully cured because cured epoxy will sand cleanly. not fully cured epoxy will gum up the paper and smear like bubble gum. don't stop until it sands clear. the other advantage is the sanding creates a nice oblique beveled edge for the glass patch.

i then used denatured alcohol to clean the area and to test the clearness of the patch edge prior to applying the patch. when you sand it, the glass will look white. if you swipe it with a denatured alcohol-soaked paper towel and it turns clear.....than that is how it will look when the new patch goes on....you will not be able to see it and it will blend right in. if you see whiteness after you wipe it with alcohol, that is what your repair will look like and you are not ready......you probably still need to sand back into solid epoxy.

trying to look at this on the bright-side, i rationalized i now had plenty of practice for the inevitable hull repair i will need to make when i eventually paddle over a rock.

   Thanks all for the expert advice, I will learn from this first experience and will apply this to my future projects. Need to get back working so that I can stay on target of 1 project a year, next up... the Kahola 14, stay tuned.....