The sash in a house of that age are designed to be easily removed. Don't make the job harder than it needs to be. Protect the glass from the chemicals and the scrapers.

For the groove you can simply use the right sized scraper bit from your new professional scraper kit.

Here is a link that might be useful: scraper kit

If there were mine( or anybody else's for that matter) Kilz primer would never touch them. You REALLY want(need) a quality slow dry oil primer for this job and Kilz is NOT it. Go to wherever you are buying your high quality paint( not Blowes or Homely Depot)and talk to the sales person about what you are doing and they will give you sound advise( something you will not get at the above mentioned big box stores)

Thanks! Obviously, I am going to have to rethink this one.

But back to my original question - how do you deal with the horizontal weathering grooves? Do you fill with epoxy?

I've used Abatron epoxy on old sashes with great success; I don't see any reason it wouldn't work in the grooves as long as they're clean, bare wood where the epoxy will be able to bond.

You do NOT want to fill in that groove in the bottom of the sashes unless there is no corresponding metal flange on the sill--this is good weatherstripping! You most likely also have those grooves and flanges around the sides of the windows.
When I first bought my house, I needed to replace sash cords, and stupidly pulled out some of the metal weatherstrip, and it is hard to find replacements for it. Needless to say, those windows now are draftier than the majority where it remains.
New replacement windows will rarely pay you back for the cost of purchase and installation--it is better to fix up your old windows--and you get to keep the original glass into the bargain. New windows just do not match the styles of old houses unless you get them custom built at horrendous cost.

Columbusguy1 - the grooves are on the face of the lower sash toward the bottom, not ON the bottom. The grooves are due to weathering; they are not part of the window design. And I'm not getting replacement windows, I'm replacing the old double pane storm windows with triple pane storms.

Oops, I meant to write, triple TRACK storm windows.

Graywings - I'm in the process of preparing to do the same project as you are currently. My house is close to 100 years old.

In preparing rotted wood for salvage and then painting, I've used wood putty. It seems to work very well. Some repairs I've made have lasted for years. I prefer the powder at water and mix type over the pre-mixed.

While I have not used this product, the website has a lot of good advice on repairing old and damaged wood:

http://www.advancedrepair.com/architectural_epoxy/restorersguide.htm

This site provides some detailed instructions on how to repair old sash/double hung windows:

http://www.sashwindowspecialist.com/diyguide.html

This site has pictures and solutions of repairing external wood with grooves and cracks due to age and weather exposure.

http://www.hereandthere.org/oldhouse/painting-siding-step-by-step.html

I hope this info was helpful to you. Good luck with your home project!

Thanks for the links, saintpfla!

You are quite welcome! Good luck on your project! :)