My B&G Vulcan 7FS failed at the helm and i purchased a new Vulcan 7R. Because its a boat, its mounting system is slightly different so I need to enlarge the hole and drill new holes. I'm thinking of using an oscillating saw to do this work and I'm wondering if anyone else has installed new instruments on those panels and how they did it?

Billy,
What's your boat name, model, hull # and location?
I've not seen acrylic instrument mounting panels on Amels (just acrylic switch panels), but maybe newer models have that. On my SN I had to enlarge the openings for my new B&G MFD's but that's in fiberglass and, yes, the oscillating saw is the right tool. On acrylic there's a risk of melting the material and getting a nasty ragged edge but you can do it by going slowly and rotating the blade continuously to avoid overheating it.
I see they want a 15mm / 19/32" radius on the corners so you'll want to do those first with a drill bit or hole saw, then cut the straight sections with the saw. 
Craig

Coder, Amel 55#56. Located in Liberty Landing, Jersey City, NJ, USA

Thanks, Billy - that was my guess and I see the 55 has that wide acrylic instrument pod. I should think you'll do fine with the oscillating blade. 
Good luck with it.
Hope you didn't get too much excitement with Tropical Cyclone "Fay" passing through your area yesterday.
Craig