NEVER use silicone on the body of a car. Silicone is acidic. The only sealant I would use is Selley's DMastic. Mil-S-8802 B-2 would probably work, but I doubt you ever wanna touch GOOP again in yer life hehehehe.
easiest way to place yer rope in is grab a spare nozzle off a caulking gun, and run the rope through it. Knot both ends of your rope so it cant fall off. All you do is start the rope, and drag the nozzle around the glass. Seats it right in the bottom of the groove. go past the point where you started when you get right around, to avoid missing a section of rubber when you pull it in.
I used to place the rubber on the screen, Rope it up, and tape the ends of the rope to the inside of the screen. I would then place a decent bead of DMastic on the seal. Lift the screen in, the slowly pull the rope, working the rubber right over the lip behind it. Do the bottom edge, and corners first, then up the sides and finally across the top. Try to avoid finishing right in the middle at the top as it is the most likely point for it to crack through with the last bit of rope. Give the window a light tap around the seal with a flat hand to set it right in the body.
DO NOT HIT THE WINDOW WHILE STILL ROPING IT IN OR THE SEAL IS COMPLETELY ENGAGED OVER THE LIP
Shove the Dmastic between the seal, and the body until it squeezes out. Then squeeze a bead between the glass and the seal. Fit your locking strip which will squeeze excess Mastic out. Push down on the seal to get that little bit extra out, which always seems to appear after a couple weeks., Clean up with Kero, and glass cleaner. All done
EDIT.........Having a second person to keep
light pressure on the window, following the rope also helps the seal seat in properly.