I replaced the two large port lights on my MK1.5 about 4 years ago, which were cracked when I bought the boat.  It sounds like yours have aluminum frames around them, so they are different than mine.  The toughest part for me was getting the old ones out.  A sharp knife and lots of patience did the trick.  I had the new ones cut by a local plastics shop using the old ones as templates.  Warren at Catalina told me that the correct acrylic for my model was 0.22" 2064 Gray, so that's what I used.  I watched a video on Boatworks Today that showed how to put the new ones in using 3M VHB tape and finishing with Dow 795 sealant, so that's how I did it.  They came out nearly perfect and haven't leaked a drop.

Erik- a little late in responding to your post, so checking on your progress. I tackled this last year with great success. Rebuilt using all existing parts except for the gaskets. Pulled the windows out completely which is really required. Found some gaps in the decking around the window cut outs that I felt needed to be filled with epoxy. Aluminum frames need to be completely disassembled and cleaned thoroughly. The channels on mine had lots of old gunk, sealant, dirt, bugs, corrosion that have to be removed before trying to re-seal. I used a small dremel wire wheel to do alot of that, and lots of acetone. Be sure to get ALL the old sealant off. I found that in the Catalina Direct kit the only useful piece is the vinyl trim strip that goes on the inside of the frame.  The U shaped glazing strip was the wrong size, too shallow, for my frames. I went to a local glass shop to find the right size.  Also don't use their sealant on the external mounting to the deck use a good quality butyl tape, like from ​https://marinehowto.com/.  Not from Home Depot. CD has a nice drawing that shows how things are supposed to be set up, print out a copy of that. The CD silicone sealant may be good stuff, not sure, I used a 3M professional product for glass. Some of the frames had corrosion spots and I could not get the nice clean aluminum color back after removing the corrosion so I spray painted with a matching rustoleum metal color which came out really nice. 
If you need some more pointers/advice on any of this let me know.  I completed all of my windows last winter and have been completely dry ever since. 
 

Thought it would be helpful to share, for all those old-school aluminum window frames still out there:
Here was my process: (you need 2 sets of hands to make this work):
1. After pulling wondows out, Completely disassemble frames and glass, clean frames down to bare metal with mechanical and chemical means. Leave no silicone or anything else behind! to make a proper seal it must be clean and dry.  Save the little aluminum connectors/screws at the joints that hold the frames together. 
2. When clean and ready to put back together, screw in both the aluminum connectors to one of the frame halves. Can't do this after the fact.  measure and cut a continuous strip of vinyl glazing to surround edge of glass (dry fit). Practice inserting the glass/glazing together into the frame channel. Make sure everything lines up perfectly. Once you apply the silicone you don't want to go back and start over. 
3. run bead of silicone inside the vinyl glazing strip where the glass will sit. Wrap the glazing strip around the glass, tape into place to hold it. 
4. run bead of silicone into the frame channel that holds the glass on the bottom half of the frame. Take the glass with glazing strip and press it into the channel. Do the same with the upper half - silicone in the channel then press it down onto the glass with glazing strip (don't forget to remove the tape). 
5. make sure frame is pressed together well and the edge joints are square and aligned. Clean up excess silicone that has oozed out.  Screw down the connectors. That's it. let it dry 24 hrs and mount on the boat.
You may want to trim/fill in gaps with epoxy around the window opening in the deck prior to mounting the windows. I found some pretty large gaps. Also may need to shim for proper alignment in the opening. Use butyl tape for the frame to deck seal. I applied the tape to the frame then inserted into opening. Some frames were a little beat up, bent, I had to bend back into shape to ensure a good fit and seal with both glass and boat (before step 2). Same with the interior trim piece that screws into frame.