If I were you I'd take off the wooden deck and its sleepers now to improve drainage. Buy a gallon of Karnak 19 and a masonry trowel at Home Depot and patch any holes in the membrane created by the removed sleepers. Remove carefully.

You're going to have to find a good roofer if you want to build back a deck on the new roof. A roofer who will know how to construct posts that transfer the deck weight onto the structure of the garage and how to flash the posts correctly. That roofer should also be able to build back a simple walking deck. A building permit will also likely be required. You could make it nice by putting up a privacy wall, pergola-type thing for shade, etc.

Or you could go the cheap route and just have a new roof put on, and then slap a new walking deck on the new roof like it is now.

A big issue is that the garage is likely underheated/unheated, as is that through-wall scupper drain. In the winter, any liquid melt off will refreeze at the drain when the temperature is <32°F, especially if it is 25°F or less. So if your garage is 45°F, there is snow on the roof, and it is 25°F outside, the heat of the garage will melt the snow, it will flow towards the drain, and then re-freeze at the drain. Insulation in the garage can help mitigate this issue.

At least $7k for a 10x20 garage in modified bitumen done properly in Chicago.