Decal Application?

I'm in the process of restoring the gel-coat on my 89 SN. I took it down to 400 and all the way back to 1,200 grit and have made my first compound pass. I have all new decals for the boat and am wavering as to what point in the polishing process is the time to apply the decals. Obviously I do not want to apply them over wax or anything other than clean chemical free gel , but should I finish all polishing and wipe the decal areas down with alcohol before application, or prep the surface now and apply them and finish the polishing with them on?
Any help would be greatly appreciated!
Here is some pictures of my progress so far!

I would be hesitant to perform any polishing over new decals. When I replaced some on another boat I had I finished all of my polishing then prepped the decal area using acetone. Your boat is looking great!

Decals - mark all of your reference lines on the hull... use fineline tape, as you will be able to see it through the release film.    I found this quote on another boat site, and have used a similar process in the past.
"A quick trip to one of your local vinyl sign shops will usually get you a couple of 3M or equal plastic and or nylon squeegies that they use and or supply with decals they produce for customers. Auto body/paint supply houses also carry them for sale to body shops and the general public. Sign shops buy them by the case for pennies and will usually give you a couple for your possible future business.
A good application fluid mixture is 1/2 bottle of window cleaner with 2 tablespoons Dawn dish detergent topped off with water. You need the window cleaner in it to accelerate the evaporation as you squeegee out the fluid from under the adhesive, so you can remove the transfer paper more quickly. This mixture is also what most sign shops use rather than the commercially available application fluid at 5 times the price.
Use masking tape as a guide, when you lay out the location of your decals for the top and left leading edge of decals before application, by placing the decal against the tape edge. It shows through the transfer paper and will peel off when the transfer paper is removed."   

I have always used a water/dishsoap solution , but I think the window cleaner idea has merit, and I would try it if I were applying vinyl.    Also to note,    once everything is where you want it, you also can spray the top release film paper with the solution you choose.   wait a minute, and the top release film will be easier to peal off of the front side of the letters without moving them.

Be aware of your outside temps, hotter temps will reduce your working time, could cause the vinyl to stretch if it is too hot.

Your boat looks great!

I just did the same last fall with my 93.....get all the polishing done...wipe down, so it's all clean...apply decals, then wax.

Thanks so much fellas!!!
After polishing before wax it is.
Also thanks for the kind words. This boat has been in my family since it was purchased new in 1989. I love this old girl and am proud to put in the sweat to make it like new again. Some of our neighbors around the lake can't understand why on earth I would put so much work into an old boat like that, boy I can't wait to see their faces when I pull up to the dock   
I will have to save a couple years to do the interior (Chritines is the best but pricey).
The advice is much appreciated yall!

Boat looks great,   I am in the process of doing the same to a 2002 Ski Nautique. I like the 2001 Nautiques,   My dad still has a 88 that he bought new,   Spent many a day behind it at the lake.