Congratulations! You bought a lovely house with a lot of potential! I own a similar small house (stuga by a lake) myself in Sweden. My house was built in 1959 and your house also seems to have been built around that time?
I find it important to stick to the age and character of the house and the setting when renovating a property like that.
I agree that it looks quite messy with the different height windows. You see that often in properties like this where people make renovations themselves without thinking of the big picture. I would recommend that you do not haste your renovation work but take a step back, just use the stuga for the Summer without doing any major work, and think carefully about how you want to use the rooms, what style/look do you like to have throughout the house, what are your renovation priorities and what could be step two etc.
Sorting out the facade should look like seems to me a high priority. You already have a door and ‘hallway’ on the left so I wonder whether you need to keep the main entry at the front? You could remove that door and that hallway and add the space to your living room, or to the kitchen (dining space?) or you could extend the bedroom (or make a walk-in closet or extra toilet?)). I would then make a glass door (same topheight as the other windows!) where the window is at the veranda-side of the livingroom and keep the windows in the corner. I really like these corner-window blocks which are so typical for houses built in 50-60.
You may later want to change the layout of the bedroom, bathroom and part of the livingroom on the other side of the house somewhat because that area seems a bit strange. e.g. make a little hallway (on top of the current bedroom- and bathroom doors door on the map) i.e. with a door to the left to the bedroom and to the right to the bathroom. This would give more privacy (and less noise from the livingroom) to both rooms and create more wallspace in your living room (since less doors).
Outside: Please keep the stone terrace, staircase and especially the railing, since so many people rip our these 50-ies details and just make a wooden decking… This makes it look so ’2000′ and the same for all houses… Is the stonewall original from when the house was built? Then definitely keep it. It is so lovely when the stone of the terrace and the wall collects the warmth of the sun during the day and then radiates it in the evening. You may want to clean/paint (lightgrey, concrete colour) the concrete floor of your terrace though.
I would change the colour of the house. Which colour depends a little bit on the other houses in the area and your taste. Off-white would look bright and fresh and would be nice against the concrete terrace. Since the house lays by the see I would avoid a very dark colour like (almost) black, which would be nice if the house would have been more in a greener area.