I think you will be needing to strip the finish if you are going to darken the stain. You should be able to do it without raising the grain too awful much, but finish sanding most likely will have to be done. The shortest way not always the best. I have not used gel stain but the old fashioned way is to remove the old finish, lightly sand with 180-220 grit. stain and then put a urethane or shellac or whatever. If the piece is flat and no turnings- you can pretty quickly sand off the finish with a pad sander and fine grit and an even light hand. There is a thread in the antique section that discussed popped veneers and the treatment. Scroll down to bottom one of the guys sounds knowledeable. And i am sure someone else can pop in here too. As for the pulls- I think you can lightly clean them up with first a damp cloth and then a dampcloth with a bit of dishsoap. if the brass is rubbed off, not much you can do short of painting or getting the brass reapplied by a specialist. have fun!

It is such a lovely piece! It will take quite a bit of time to shop for matching hardware, and it would be less costly for you to do the online search yourself. You might want to find matching bail handles for the four lower draws, and a new lock and front trim, while saving the old parts tucked in a drawer. The finishing and lacquer would be done by a furniture restoration company. Interview a lot of restorers after reading online reviews. How fortunate you are to be so close to a large metropolitan area. Send pictures and/or bring a drawer for estimates and suggestions. I did see a site called Chineart.com with catalog pages of oriental hardware. No idea if the products come from China or anything about the business, but if they have catalogs, so do a hundred other stores and sites. Best of luck on your project. I am attaching a list of furniture restoration companies in the Chicago area listed on Yelp. You should also be able to get recommendations for repair companies from antique Asian furniture stores. It is going to be beautiful. :) https://www.yelp.com/search?find_desc=antique+furniture+repair&find_loc=Chicago%2C+IL

I am not sure I would call it a defect, fill the joints and paint it again I would not paint it black unless you want to call attention to it.

I have done things like that on top of wood dressers. To do that floor, it's just taking the wood down it's natural state, taping off your design, and applying the stain to that portion of it. Then the entire flooring gets the clear coat. (the other part stays natural) Is it something you could do? yes, but it's a lot of work. The time consuming part is measuring and taping. takes many, many hours. This one was actually a floor paint, not a stain, but you would do the stain in the same manner. There is a link to this one if you're interested in a DIY! Is it something you'd be willing to pay for? not going to lie, based on the size of the room it could be 1K-3K. is that worth it to you? You would have to call a specialist in wood finishing and borders, not a flooring contractor. Someone who specializes in staining wood borders. I would think for that price you could have your flooring specialist cut out a ribbon of wood and inlay a darker species in there. Another option is to prep the same way, but instead of stain use a real milk paint. you could do any color. (need to be on raw wood though). same clear coat application.