Adjusting the length of the rub rails

I’m getting ready to reinstall the rub rails on my 1940 Chris Craft Special Race boat.
However, it appears that during my restoration the length where the rub rails go got about 1/2" shorter. Do I just cut it and countersink the hole for the last screw where the two section meet?
The existing screw holes are pressed counter sunk in the rails. I’m not sure how to replicate that or if it is even necessary.
Thanks for any help.

This is a pitty responce, since there is a bit to unpack here. Shorter? Anyway, I would counter sink it to match. The screws want to be flat with the rail so they dont catch on anything. Also, while you at it, make sure its not a philips or Reed and prince screw, it should match. You can also replace the rub rail. Need a pic

Not sure why the wood gunnel is shorter, but it sounds like you will be drilling new holes for the rail screws. If you don’t already own one, purchase a Vix bit (also known as a self centering bit) of the correct size. Makes getting the screw in the center of the rail hole 1000 times easier.
vix bit

Did you look at trimming a little off the other ends of the rub rail? Do you have the wood backing under the stainless rub rail?

See picture.

This project was a complete rebuild, replacing 90% of the original wood which was broken, split, rotten or otherwise not useable. So all new holes along the rub rail. I’m going to have to get me one of those bits.
I looked at trimming the flat end but the holes in that area are within about 5/16" inch of the end. Yes I have wood baking under the stainless steel rub rail.

As far as using the Vix bit; I purchased all 3 sizes, (ya never know what else you might one day do) and with the rail in place bored about a 1/2" deep hole letting the bit center in the rail hole. To finish the depth, I used a tapered bit of the correct diameter to match the screw, because the length of the Vix bit won’t get the hole deep enough, it will just be centered as you need it.

We always replicate the spray rails to the correct length and then install them where they belong bedded in 3M 4200. Bedding combats future rot. Use 4200 instead of 5200 so they can be released if/when necessary in the future.