Very hard but can be done.I made a special tool up to hold the clips and then tap in with small hammer'
usually I put clips in then glass then the felt.
at leat 5 per side on fronts 4 on rears
full set of u channels and fuzzys for side of glass $200 full kit
Gord is right about it being a pain to do with the glass in but I do it by hooking the clips to the fuzzy strip, jamming the assembly down between the glass and the body then pulling the clips in place with something called a right angle awl. Such an awl is usually available at hardware stores with one end straight and the other bent to a right angle. Not a fun project though and it takes a bit of patience.
I don't think you'll be able to drop the window down further because it will hit a stop on the bottom of the door. Use that right angled awl and with a little bit of swearing and patience you'll get the fussy strips in.