I replaced my starboard side ones last year. I used a utility knife on the inside seal to get the window out. Once I was able to get one portion free, I would push the window out a bit to expose a bit more of the sealant and cut that with the knife. The PO had used silicone on them so it wasn't too bad to get them out.
Then spent a while with the utility knife, paint scraper and acetone & goof off to try to get rid of all the old silicone.
My windows were really crazed so I brought them to a local plexiglass shop and the fabricated new ones. The inside edge of the window is beveled. The plexiglass shop couldn't router the correct angle so he did it as much as he could. I then took a grinder and ground down the edge all the way around. Took a few tries. I would grind, stick it into the frame, see where it didn't sit flush then grind some more. Once it sat flush, I took some black 1/2" wide by 1/8" thick foam gasket. One side was sticky so I cut up a bunch of pieces and placed them every 6-8" around the window frames. This keeps the window off the frame and gives a gap for the sealant so it all doesn't get squirt out when you put the window in.
Then I took blue painters tape and taped off around the inside and outside of the window frame for any sealant that spilled out. Then I filled the whole recessed area, that the window sits in, with black Dow 795. I used almost a tube per window. If you don't use enough you will get void and can see them through the window. Use more than you think you will need. Whatever squirts out will just go onto the painters tape around the frame. Make sure you tape off a couple of inches thick on the outside. The black sealant gets everywhere.
Also, leave the sticky paper on the plexiglass frame (if you get new windows) If using the old window, I would tape off a good 2-3" around the edge of the window on the inside and outside. On the inside, you need to leave about 3/4" of the window exposed around the edge. This is where it will sit in the sealant. Since I had new windows with the paper, I put the window in place, traced the outline of the window frame on the inside, then used a razor blade to trim that amount of paper off to accept the sealant.
Once I had the sealant on the frame, I put the window in place. I found if I pushed on the window it would sit tight but then slowly start to lift off. Not enough to fall out of the frame but enough that it was noticeable. You would need to rig something up to keep pressure on it until the sealant sets. I ended up putting a couple of screws around the window to hold it in place. The screws are small and look fine. Once it was set in place, I used my finger around the edge of the window to smooth off and push in any sealant that squirted out when the window went in.
After and hour or so, the sealant starts to set. There is an outside skin that is dry but if it's a thick blob, the inside will still be mushy. On the inside of the window, I took a razor blade and sliced off any sealant that had squirted between the window and frame.
Waited 24 hrs then pulled all the tape off. Since I had taped everything really well, there was almost no cleanup needed.