Hi Tim
Did this on my 'van last year and whilst hard work it was very satisfying to know it was done well. When I took the window rails off I was amazed at how the amount of sealant varied from place to place. Clearly the manufacturer had not seen fit to make sure a uniform amount was applied.
As regards the screws these will rust out quickly if they are steel (usualy plated) and then put adjacent to alluminium. Ask a Land Rover (alluminium body on steel frame/chassis) owner about the electrolitic corrossion that takes place between steel and alluminium if not separated by an inert substance such as a rubber sheet! A steel screw, sitting on alluminium with a bit of condensation on it will set about rotting itself to blazes in a very short time.
This is what I did on the advice of the place that I bought it.
Remove the windows - mine just slid out once the retaining stops were removed. Grind off the head of the old screws if they will not come out easily and take of the rail.
You can then get at the stub of the stubbon screws with molegrips or similar but DO BE CAREFUL WITH THE 'VANS PAINT - it is very thin and easily scratched.
Once removed the hole can be filled with sealant (not silicone - see later), however I did have to admit defeat on a couple and simply ground them down flush with the surface and had to be satisfied with painting the bair metal with Kurust. I know where they are and will be checking then regularly.
Now using stainless steel screws of the same size as the original (available from Towsure and other places) I refitted the window rail using a "healthy" amount of sealant and redrilling pilot holes equidistant between the original holes. The old holes were checked to make sure they were nicely full of sealant and new stainless screws use here as well. Using the old screw holes as "markers" allows for an exact line-up when drilling the new holes. The job was finnished off with new plastic strip covering the screws.
I now know that as well as the original screws are out and replaced with stainless, the rail now has a fixing screw about evey 9inches rather than evey 18 inches and that it is well and trully sealed against the elements.
Because I took it slowly the first window took an afternoon. The next day I went back and did all the others by lunchtime.
I checked the awning rails on mine and they were ok but I did run a bead of sealant all arround them to make sure as well as removing the sealant strip to check the state of the screws which interestingly compared to the window ones were in excellent condition.
I plan to remove both rails this summer (I do not use my 'van in the school summmer holidays) and redo the sealant just to be sure.
As regards the sealant to use I was strongly advised not to use silicone as it is difficult to remove if required and as another contributor has mentioned on another thread - it is difficult to reseal again if you have to.
The stuff I used was given to me by the dealer I bought the van from (Blackmore Vale @ Shaftesbury 01747 851497- very helpful and I would recommend them) and is what is used in their workshops. It is like a mastic and never sets unlike silicone which does and then can split with the movement in a caravan.
The job is messy but VERY satisfying.