I can smooth things out during final finishing. I have a few questions about generating a smooth finish. Since I can't do a complete coat, top and bottom, should I use painters tape to purposely define a stopping point just below the seam? Should I use the fast curing resin at this point, I assume this is a yes? Should I apply the final coats with a brush or roller? Since it is December, 50F in California, is it okay to do the final finishing at this temperature?

It is the sanding process that wears the high spots down to the low spots.Filling the low areas up to the high ones adds unessesery weight.Make sure that even the low spots are scuffed (no shine)if mechanical bonding for the next coat.Avoid scuffing into the weave(as much as possible)After this you may find that your next coat is the varnish,if you have not cut through to the cloth (to much).You would sand the whole boat all together.Worth washing ,with just water ,to remove any wax,dust,blush or whatever before coating.Don't bother with masking tape but if you have to coat it in two halves just " feather" the edges of the first part of the coating to avoid creating a distinctive step for which you would then have to address.Coat the second "half "overlapping the first,without sanding,if chemical bonding.
Use whatever tool you are comfortable with,for coat application and use as little coat volume as it takes to avoid runs but enough to evenly spread over the surface.
For cold temps,I have used a hair dryer to condition the viscosity of the pre warmed coating fluid ,when on the surface as you apply it.You could pre heat the boat surface area immediately "in front "of the coating.You may consider using a helping hand with this part.This is what I do.Others may have better ideas.