Cost to build a garage will vary and you can expect to pay around $50 per s/f. But still – how you are planning to finish it is the most important factor. Finishing exterior walls with a vinyl siding is a one thing, but brick walls will be much more expensive and so on… If you have a drawings...
I do not think it is a special window for brick walls a long as they fit in the opening, but if you are laying bricks it should be a support from the top of a window opening.
Attach the window with insulation foam...
Are you using that free version of Google Sketch Up? I checked ones and it seems very limited, or I just didn't go far, but from your drawings looks like it is possible to make a decent design.
If covered spots are not changing color, but the open area is - it is LIGHT and doesn't have to be direct sun. Some products more sensitive some less, like paint or wood floor. If it is a chemical problem - the whole floor would change the color.
I used this and have no complains.
<a href="http://www.homedepot.com/h_d1/N-5yc1v/R-100566183/h_d2/ProductDisplay?langId=-1&storeId=10051&catalogId=10053">Oil finish</a>
Do not know kind of expensive, you can try some cheaper products, but oil based, and do it 3 times.
Had similar problem in basement not sure what it is but the guy cleaned all that mess and pour self leveling concrete on top. We painted with epoxy one room where the storage is - no cracks still rest area under the laminate so not a possibility to check.
Do not know how much you can spend...
We have a basement with cork click an lock floor. Children like it and it is for over 3 years - didn't have any problems yet. But yes you have to be careful moving furniture on such floor.