Yes the weep holes should be cleared out. The weeps should be enough so the filler piece can remained caulked to the sill. A heat gun should not effect the storms, but why are you using a heat gun?

Use a thin-bladed screwdriver to poke through the weep holes from the inside, and maybe score the caulk at those points from the outside with a utility knife.

I need to repaint the sills and jams. The existing paint is alligatored and or missing. Doesn't it need to be removed prior to putting on more paint? I was hoping a heat gun would help with the removal process. Unfortunately, there seems to be a layer of thick tan colored stuff under the paint. I found it on one of the doors which had never been shellaced too. This stuff does not come up easily with a heat gun. I'm going to have to find a different solution.

Mary, I suspect you'll have better luck if you remove the aluminum storms entirely before beginning work. You can clean and de-gunk them once they're down, and stripping the sills and jambs effectively will be well-nigh impossible with that aluminum still on. They're usually attached with a few screws and aren't supposed to be caulked on, although many homeowners over the years haven't known this and you'll likely find them covered in caulk. Get 'em off before you start stripping, and your job will be MUCH easier.

A great resource is John Leeke's Historic Homeworks windows forum:

Here is a link that might be useful: Windows Forum

My parents' house had aluminum storms (which I loved) and wood windows. I left the storms in place and removed the windows from the inside (carefully removing the trim). That way you can easily work on the glazing while the storm windows protected the house from rain, etc. You'll be able to see the entire sill, have more room to strip/sand and can paint the jams on a flat surface. I used replacement window channels that added made the windows much tighter and easy to operate. Glazing is no easy job and I can't imagine having to do it from the outside on a ladder.
Remember, if you need to replace the glazing, you need to prime first with an oil-based primer, another joy from the outside on a ladder.
You may need to re-think your process. It sounds much more complicated than it really is.

I second the reccomendation to take the storms off for your stripping project. You can bed the aluminum frames in caulk on the top and sides with impunity, but exercise caution along the bottom. If, after removing all paint and caulk from the mating surfaces, if the bottom still has a gap you can see light through at almost every angle, then caulk it from the topside only, leaving at least 2 half-inch gaps for stormwater that infiltrates to quickly run out. Do not caulk along the bottom, as that creates a water trap above the caulk line, exposing that vertical edge of the wood sill to longstanding exposure to water.
Of course, your window frames may follow a different pattern to what I am familiar with; if your bottom piece of aluminum contacts the sill at one point (perpendicular) then there is no water trap and you can caulk it, but leave two 1/2" gaps for water to escape.
Getting your windows restored so they can be lifted with one finger is one of the (few and fleeting!) joys of old house-ownership.
Casey

Thank heavens my windows do open with one finger. This was such a pleasant surprise a year ago, once we had banged on them a little to get them loose again.

Right now, the task is really maintenance, not repair. The paint between the sashes and the storms is badly alligatored, peeling or simply gone. I bet it had something to do with the space being totally sealed for so many years. I've already opened up the weep holes and now am tackling the paint.

I'm torn on how to proceed because I was counting on taking out the sashes and using the storms as the window. But I like the idea of having all the room I would get with having the storms out too. The ability to do most of the work from inside is also nice. So now I'm leaning toward taking the sashes and storms off, working on the alligatored paint on the jams, and then priming, repainting and putting the storms back up as quickly as possible. I guess I would need to use plywood to close up the opening at night.

Then once the storms are reinstalled, I would start on the sashes. All glazing would be done with the sashes on a flat surface. Which raises another question. When does glazing need to be replaced? Meany suggested just smearing more glazing over cracked areas. What about small areas that have lifted?

Casey, my the bottom of my storms sit on the flat part of the window sill. There is an adjustable filler piece that the aluminum frame sits in. I can move the filler piece up and down a tad without doing anything to the frame. This filler piece has three 1 mm holes near the bottom edge. I will caulk leaving 1/2" gaps around the holes for additional drainage. Should I caulk both inside and out?

Thanks all for you help!

Mary, I'd not bother to remove the wood sashes at the same time as the storms, you never know when a sudden storm will come up. :)

The nice thing with double-hungs is that the uppers can be moved down to work on the jambs and frame from the inside, thus not needing to remove the sashes unless they need repairing themselves. Alas, some of my uppers have long been sealed up with some caulking on the ouer faces, and probably a nail or two--particularly the ones in my attic--1 over 1 on the side dormers and 4 over 1 on the front dormer. :(

My sills are in the same condition as yours with the alligatoring and missing paint inside my nasty aluminum storms...but it seems none of my jambs were ever painted--they have the integral weatherstripping still intact!

Hi,
Do the outside work first, reinstall the storms and remove the wooden sash, then it will be all done. Or reverse the order and do the outside later.
Casey