I was going to do the same thing and here is the conclusion I came to for my Bav 40 Ocean. The large rutgetson top hatches I replaced all 3 with Lewmar 60's. This was absolutely the right choice for me. The old hatches were all leaking badly when I bought the boat and I started by taking one of them and taking the lexan/acrylic lens out and re-seating it properly. The rutgerson hatches were built really strongly but I didn't like the way they sealed into the stainless frame so replace I did and never looked back. You may have lewmar hatches already on yours already depending on the year. Its and easy do it yourself project with a little patience.
Regarding the port lights - that's another story. The price on replacing those is cost prohibitive. My last boat I replaced all of them with new found metal stainless ports. They were claimed by the NFM manufacturer to be a perfect fit and and easy job. Over 40 hours of my labor later and a lot of cutting and grinding fiberglass I finished the job. Came out beautiful but way too much work. On the Bav I have the rutgerson ports which were in bad shape and leaking. I removed all the inner trim rings, sanded, primed, and refinished them with a metallic paint and they looked great. Then I cleaned up the ports themselves which are all heavy stainless and well built and all was well. when I started looking into replacing them they prices were ridiculous. And after going through the pain on my last boat I was very happy with the refinished results of the rutgerson ports.
The butterfly hatches are another story. I contacted Bavaria to replace my 2 butterfly rutgerson hatches and they sold me lewmar replacements which I was told would be a perfect fit. My mistake thinking they would be able to sell me hatches that actually fit MY boat. I guess I was spoiled with my last boat that was an Island Packet. They kept meticulous records and even after 25 years when I needed a part they would send the right one. In fact I even got the chance to talk to the gentlemen who built my boat on numerous occasions. Anyway...back to the buttfly hatches. After I purchased them over a winter I didn't get to install them for several months. When I finally did they were an inch too short. So I took the time to fully refurbish the Rutgerson butterflys and re-seat all acrylic. They came out great just a big pain in the @#$ to do. We just had hurricane sandy a few months back and the boat sustained 90mph wind driven rain and was dry as a desert. I guess I did it right.
If anyone is interested in 2 brand new lewar side hatches (I call them butterflys) let me know. I paid $1200 but am willing to give a 2 for 1 special. $600 for the both + shipping. Anyone interested I'll post pics. They are custom made by Lewmar for Bav and came from the Bavaria factory. If you already have lewmar hatches these will fit. They will not fit as a Rutgerson replacement.
So I've given you my 2 cents (ok that's more like 3 cents). Good luck in your quest but think about refubing before you spend a lot of money from your cruising kitty on ports/hatches.
