I've done this type of decaling on some Amfleet cars and I know how tricky it is, so here's my technique in case you're doing something differently. First of all, you really need to make sure that the decal is completely dry, otherwise you risk accidentally moving it in the process of trying to cut it. Second, use a brand-new sharp X-acto blade to eliminate dullness as the cause of your problem.
Even after doing everything else right, I agree that there's a tendency for the decals to rip and crack as you cut them. This is actually okay as long as you make your cuts at least 1/32" inside the edges of the window openings. To help make complete cuts before the decal sags too much to use the knife, I partially cut opposing edges in opposite directions, leaving the scrap decal piece attached at the corners, then slice quickly through those corners to remove the piece. This leaves ragged edges around the inside of the window openings, but you can apply Micro Sol and then gently prod the edges to make them curl around and cling to the inside of the window opening. Several applications may be necessary, especially if the car you're using has molded window frame detail that the decals will have to settle into.
Once the decals are again completely dry, you do have the option of using your knife to carefully scrape the excess decal film from inside the window openings if you're afraid that the window glazing will knock the bits of decal loose anyway. If having decal film inside the openings is not a problem, you may simply need to use some black paint to line the inside edges for a uniform appearance. When you're done with all the decaling, I suggest using Microscale's Micro Satin clear coat to seal the car. It allows silver paint to retain its metallic appearance, but gives decals a more subdued finish that helps make them look painted on.
You're right that airbrushing would make this job much easier on your Comets and Amfleets. If you don't have an airbrush, you could at least use black spray paint for your Comets to save time. I wish I could just mask and spray the stripes on my cars, but trying to get consistent widths and sharp edges for Phase III striping would be tricky enough that I just stick with the decal stripes.
