The layout looks great so far! You're doing a great job!

1. I would leave the peninsula area open so you can keep your kitchen feeling bright and airy. Putting upper cabinets there will make things feel closed off. Not as closed off as the wall you removed, I'm sure, but still would remove the open concept feel. I would put some storage solution on the wall with the window, though. Maybe just some open shelving? (See images)

Also, I would make sure the cabinets go all the way to the ceiling, rather than have the boxes up top. Even if it's hard to reach, it's better than the wasted space of those drywalled boxes.

2. I think you could go either way on the vent hood, but I like the idea of the wall mounted one in your space. It would really modernize the room. However, functionality is key in a kitchen, so before you go that route, make sure you have enough storage space. If you need the cabinets, then go for the under mount.

3/4. I think you can definitely do a coffee station over on that other side of the door. I do think you might regret putting your microwave there, though. It's kind of out of reach, and might eventually become a nuisance to have it so far separated from the rest of the kitchen appliances. If you have open shelving on the wall with the window, perhaps the microwave could be placed there somewhere? Just something to think about. Aesthetic wise it doesn't look bad over there, so if you don't use the microwave much, you could probably get away with it at the coffee station. I'm a microwave fiend, though, and having it far away would get on my nerves. :) A wine cooler over there would be perfect, though! You can make that area a coffee station/dry bar.

Good job so far! Keep posting updates!! :)

Thank you so much for taking the time to respond Emily. I'm going to implement several things you've mentioned in your post. This project was supposed to be a lot smaller in scope, but as things progress things keep getting added. I completely agree with having the cabinets go to the ceiling and perhaps adding some shelving on the other wall. I will post pictures once the remodel is complete.

Rusty, I thought about it, but when we took up the brown tile near the front door we had to pour 28 bags of concrete to fix the mess underneath. When you say build up a "simple subfloor" is it really simple? I can look into it. Wouldn't the sunroom on the other side of the french doors not be level as well? This is the view of the room from another angle.

Coffee requires water. I would forget thinking of it as a coffee station. I do like the cabinet and the microwave. I like the micro to be near the refrigerator, and it looks close enough to my eye. Of course, if you don't mind schlepping water across the room then it will be a fine coffee station.

No cabinets above the peninsula.

If you changed the coffee station idea to a full pantry, you might have room on the other side to install the micro in the lower cabinets. Pantry or coffee station? I'd choose a proper pantry every time. Try to have a counter depth fridge too.

I have the same layout as you. Minus the bar area. I had an independent cabinet on the left of the window. But I got rid of it. It was taking too much visual space. Plus the person sitting at the counter near that area had it hanging over their head.
I will be installing book ledge instead. For me, if money wasn't an issue I would put a window instead.
I love your bar area. In a perfect world I would put a sink there too because you don't want people to go back and forth to the main sink for filling/washing the coffee machine. The wine fridge will be great there too.
Trust your gut. You are doing a great job!

Agree with no upper cabinets over peninsula. But that will probably leave you short of storage space. I agree with nixing the coffee station too, for the same reason. I agree that area would be better used for added storage, like to put in a large lovely wall to wall buffet and hutch. You can just use your kitchen cabinets to make it, uppers and lowers. That will then be able to function as a coffee station, should you so desire, but also as a serving buffet for large gatherings.

I would reconsider the island. One like this would work perfectly in your space:

Update

looks nice! great job. suggestion to the left side of the window, if I may? some wood shelving> sconce over the window would be great too!

A microwave above the stove would not be practical. The "exhaust vent" for your range should be powerful and should vent smells to the outside of the house either through the wall or through the ceiling. Microwave "exhaust vents" don't vent outside, and having a microwave over the stove gives you one more surface to try to keep clean. A stainless steel vent hood which is properly ducted to the outside would be my choice.
I like having the microwave on a counter for easy access and ease of removing hot dishes to place on the counter or on a trivet. A coffee station is a nice feature. A coffee maker, coffee (ground or pods) and cups or mugs in a nearby drawer or upper cabinet is convenient. If you use cream, you could store it in a wine fridge in the same beverage zone.

My microwave above my stove vents outside. How it vents just depends on which kind you buy. I prefer to have the microwave over the stove to leave as much counter space free as I can. It is an individual choice.

Mine vents outside as well. It could be set up either way. But it does not draw as much as I would like.

I hid the microwave in the pantry to the far right. I created shelving in there and added an outlet. a little bit of an odd location, but it freed up my counter space.

Wonderful job! Love that you hid the microwave... I haven't owned one in 12 years and have never missed it.