https://share.icloud.com/photos/0acS5NOYdGyG_OG-cZkHstOQQ

That pic shows a p-joint that's fine structurally but wasn't clamped flat during assembly and epoxy curing. You can add more epoxy - in fact you should - to both seal the scraped-clean veneer as well as bring those bare surfaces up to the same level as the areas showing epoxy adjacent that're higher.

Somewhere on a post I made a year or more here I showed how I used wood cauls atop my p-joints to bring the two pieces into the same plane during assembly. Surfaces end up matching levels very nicely this way, any excess epoxy's also more uniform in thickness and easily scraped away. What you have there isn't as neat but isn't structurally flawed, just needs more attention to bring the bare areas up to snuff.

I'll try to re-post those pics here, prolly easier than trying to find a thread from over a couple years back in time....

   Thanks.  Do I have to worry about a cosmetic difference between the epoxy here not matching the overall epoxy when I glass the boat?  

"Do I have to worry about a cosmetic difference between the epoxy here not matching the overall epoxy when I glass the boat?"   

No, not really. Too much epoxy, unevenly applied, can get trapped under saturated cloth and cloth will float, potentially trapping air bubbles underneath. Fiberglass cloth that's fully saturated with epoxy resin then carefully squeegeed flat ought to be virtually invisible.

Some folks like to apply cloth to bare ply then add epoxy, then spread that around with a plastic spreader or roller. This can lead to outgassing from air that's in the ply, which will leave bubbles under the cloth. I find it's less of a problem if raw ply is first coated with epoxy then allowed to cure, then lightly sanded & wiped clean of dust before cloth is placed. That way the ply's sealed so there's less chance of bubbles to form under the cloth.

P-Joint assembled under cauls & shims

P-Joint glued up w/ cauls removed, still under plastic release liner

P-Joint after careful scraping

Several P-Joints before applying resin

(Here's hoping these show up! Without an edit button it's frustrating sometimes getting images to reveal themselves here....)

the colors should match once everything is epoxied.

that said, i looked at your pictures and it will be very important to use denatured alcohol to ensure you get the sanding dust out of the little holes (that are white becuase they have dust in them) or else you next round of epoxy may just seal the dust in leaving you with those little white specs that can be unsightly.

i would get a little cup of alcohol and a toothbrush to scrub it in to ensure you get the dust out.  if it turns clear under the alcohol....you are in good shape.  you should also be attentive to the dust disappearing when overcoating it with epoxy.

to minimize the chance of further problems, i would actually do the cleaning and an overcoat of epoxy now.....before glassing to get rid of the dust/bubbles...sometimes it is very difficult to do that when at the sametime applying glass.

h

My point being to show how p-joints glued up with pressure holding the tabs flat leaves a finished joint looking like that image the second link above brings you; epoxy's fairly even across the finished, jointed surface, fairly easy to use a cabinet scraper to remove excess if need be.

To your question about cosmetic difference: there shouldn't be any once you've epoxied the entire surface. The plywood gets saturated whether you simply add additional coats or add fiberglass cloth and epoxy where indicated in your plans.

Hope this all helps you! You're doing fine from what I can tell, carry on! 

Side note: I'd forgotten the feature here that brings you a history of a member's threads when you click on their underlined name above something they've posted.

Thread I was hesitant to go looking for is easy enough to access from my history, or this link: https://www.clcboats.com/forum/clcforum/thread/45519.html

   So you did take the time to scrape off all the excess epoxy.  

Yes, at least enough to ensure that there'd be no hard edge telltale left after adding epoxy & perhaps 'glass over P-jointed areas later on.

If the epoxy escaped onto surfaces uniformly w/ no bare spots it could be thinned by scraping, attention being paid to the edges where it can be feathered out to bare wood. There's little benefit to scraping all the escaped stuff off for the extra labor needed and the risk of going into that first, thin ply veneer layer. That last bit's why I don't advocate sanding; you have more localized control using a scraper than when sanding.

Take note too whether a 'bright' finish is planned. This'll suggest more care during assembly so the resulting structure is not only as transparent as possible but also as smooth and uniform at the final surface. If painting's the goal you don't have to be as fussy over cosmetic details (structural's always important!) while you're working towards a smooth, uniform final surface for paint.