I've stained various parts of 3 different boats.  Never had your problem of water drips, but have had to do the "match" effort in areas where I had to sand through stain (even in areas that were stained and epoxy coated prior to assembly).  Matching is certainly difficult, I found it best to start with dilute stain and keep working slowly by adding more "wipe overs" to the lighter area of the  match until the colors came close, and avoid adding any color to the darker edge of the area being matched.  And let things dry to know whether the match is true.

In your case (no epoxy anywhwere on your pieces) I might first try to do a color match in the area of the drip spots, not working to get it perfect, just to get a nearly uniform starting surface.  Then sand the WHOLE piece until it was much lighter than desired (and by then the spots are hopefully almost not noticeable).  The stain doesn't relly sink in all that deeply, thus sanding will remove most of the color in a big hurry.  Then restain the whole piece until the desired color is restored (and by this time hopefully the spots are no longer noticeable at all).  Add stain until the color (hopefully) matches the color of other major pieces of the boat that you haven't had to fix.

Good luck.  More advice you don't really need: topcoat stained peices with epoxy just as soon as possible during the build - and fix the roof leak.

The stain CLC sells for this is solvent (alcohol?) based. Other stains are water or oil based. Solvent based is the right choice because of compatibility with the epoxy. I have found getting it right with solvent stains more tricky - it takes more care to get uniformity whereas other ones seem to even out just with more rubbing back and forth. Bubblehead above refers to this problem.

I am hesitant to give advice. You need to decide what risks to take. So many times, fixing a small problem just makes a bigger problem. First, I would get a sense for appearance after finish is on the affect part - wipe over with solvent soaked rag. For a few minutes you will see if the stain actually shows up badly. In my experience, dry stain problems look way less once they are wetted.

Option 1

I would recommend lightening up the affect region by taking a solvent soaked clean rag (e.g. denatured alcohol on teeshirt rag) and rubbing it over the region. Then, later, once dry, restain it. You will try to make it even. When it dries it will not look perfect. However, in my experience it looks better when finish is put on it. You get a sense for that if you rub an alcohol soaked rag over the entire region.   You can use repeated rubbings with a clean alcohol soaked rag to try to smooth out deficiencies but this is more difficult than it sounds. (You can try diluting the stain too - that's worked for me but you are on your own risk wise.)

Option 2

Review the CLC advice on the topic very closely

https://www.clcboats.com/shoptips/finishing-tips/staining-your-kayak.html

Curiously, the advice for fixing small stain defects is to use a Q- tip - on a boat? This tells you something about how hard it is to get perfection.

This is because of the problem above - this particular stain tends to just build up depth and not even out if you are not careful. As I learned, solvent based stains even stain epoxy (oil and water ones wipe right off). Logical but I wasn't quite anticipating it.

Option 3

Bug into feature. A CLC favourite for major incidents. Paint a bold colored stripe over the region.

https://www.clcboats.com/shoptips/epoxy_and_fiberglass/surviving-catastrophe.html