Lenore, who is installing the granite slab shower? Start there and make your priority be hiring a VERY experienced tile professional - one you have vetted carefully to insure that their qualifications meet your design requirements and product selections. Stone slab installations are not for the B team, and especially in a wet area. Can it be done? Yes, depending upon the structure over which a solid surface stone is installed and the methods used. We install solid surface shower walls regularly, but from an empty cavity which we build to meet all specific design and installation specifications, including the pan. A solid stone slab cannot be supported by the pan (it is not meant to support a slab wall). A slab wall is pinned and tied so it is self supported, not supported by a pan. This is a very complex installation. A LOT to consider. As one example, the thickness of your slab? 2cm. 3cm? (effects the weight load on the space). And I could go on. After you have carefully vetted the qualified tile contractor, have this conversation with them. If you question or want to clarify their recommendations, check back or seek professional advice from other qualified sources. Please consult with a professional onsite. Good luck with your project.

"For the backer rod, do you simply caulk that in place or is there another form of attachment method that I should use first? " It should be large enough to require forcing into place before covering with caulk. About 505 wider than the gap seems to work well. If you need to you can even split the rod using a sharp utility knife. Uneven gaps can be a PITA to fill. the backer is just there as a base for the caulk, so using separate pieces as a long gap varies in width is not a problem (except for installing it). if any gaps remaining are small enough, caulk will not get through them badly anyway. Tiny gaps at mortar joints (less than 1/8 inch or so) can usually be tolerated. Part depends on how thick (viscosity wise) the caulk you are using is. A smooth caulk surface will look better up close, and if you apply it carefully ad too it smooth can look acceptable. You get some relief on second story work since no one normally can get close enough to see it well (but around a front door or ground level window looking onto the front steps needs to look nicer).

If you caulk is LATEX-based (siliconized or otherwise), the trick is to use a wet rag or sponge to frequently clean your finger as you go. If you are NOT using something that's latex-based, then a steady hand is key, perhaps immediately "tooling" once (flattening with a small putty knife, for example), and mostly leaving it alone. For big gaps, first fill with "backer rod", which is basically the grey polystyrene rope insulation they sell. Comes in a couple of thicknesses (1/4", 5/8", etc)

So they sealed them in? Why? Because they were leaking air? Security? Its hard to know what happened without pictures. Also, I have seen many compounds referred to as "putty." So if I was a tenant and my windows were cold and drafty and leaking heat I might run a bead of caulk to seal out the cold. In which case most caulks can be pealed off without too much trouble. If it truly is a gooey putty smeared all over...yuck. Do you need new windows?