Bump! :)

I think it's fine--even preferable--to put the clean-up zone on the side wall, but I'd suggest keeping the prep zone, with a smaller sink, on the island. Helpers can load or unload the DW, or gather dishes to set the table, without entering the primary prep/cooking zones. Assuming you still want access to the formal DR from the kitchen, there is space for an opening by taking a few inches from the pantry. I'd put the fridge near the breakfast area, so the cooktop/hood are m/l centered from the great room. Wall oven and MW can go in the location you suggested, but I'd make that a serving counter to the right, with coffee, toaster, breakfast items, etc.

Personally, I think I'd reorient the island and put the fridge on the bottom left corner, closer to the living areas and stairs, but you'd probably need to omit the step-in pantry/servery and use ROTS on the top wall.

ETA: Here's a basic, messy version of that option, but you'd need to work out the corner of the great room with the architect. There's more distance between the fridge and cooktop, but the fridge is much more convenient to the living areas, so it's a trade-off. Your template has a small fridge outline, so I think maybe that should be wider, and narrow pantry omitted, and pantries adjusted in the first plan:

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Discussions--Extra-deep counters

Thank you so much! Those are both great suggestions.. we did not think about changing the orientation of the island.. it can definitely work to our advantage. And love the idea of making a serving counter, it will help with not having the counter space end abruptly. Especially if we add 1 pantry to the end.
You are right, the fridge outline is way too small. We are hoping to get a better floor plan thats to scale. It will help in deciding so many changes. 
Again, thanks for your insight!

You're welcome. I had a bit more time to spend on the second plan, so this is more detailed. The island is not as deep, and it's moved toward the perimeter cabs, so the corner of the great room is intact.

I'm posting this as a rough example, but I have to say that I don't really care for either plan. In the first plan, the fridge is too far into the kitchen, the clean-up zone is too far from the prep zone, and the oven is in the breakfast area. In the second plan, the fridge is convenient to the living areas, but too far from the cooktop. Although the oven is in the kitchen, it's a bit too far from the prep area, IMO--but if you don't use the oven often, maybe it would be OK. You need to keep access to the DR from the kitchen, which breaks up the shorter wall of the L.

BTW, can you add windows to the exterior kitchen wall? Even with the large windows in the adjacent rooms, I think that long wall needs some natural light.

I know you don't want the clean-up sink on the island, but here's another version with the original island layout. If you choose to have the coffee/breakfast area between the pantries in the breakfast room, the whole area below the fridge could be dedicated to pantry space:

I hope others will have some ideas for a functional and attractive kitchen.