Alex you could make this work as long as you are totally clear to westerners what they are getting. As you can see, many readers don’t understand Tokyo. And in comparison to the big hotels in your area, yours is a good deal. The capsules can get sold out, which makes yours an option for that sort of budget customer who can’t deal with the capsule situation or hasn’t heard of it. I only stayed one night in the capsule, but my son stayed several days and was just done with the idea he had to check out every day even though he had a multi day reservation. A big pain in the neck. I don’t think he would do a capsule again. Also his floor wasn’t as nice as mine. 
As for marketing…I was just thinking…Japanese job hunters are a big capsule customer… Is there any way to reach those types? If you get Westerners, what about offering to meet them at Shinjuku Station? Someone arriving might feel very intimidated by the crowds and feel lost. I had to hold my son’s hand so I wouldn’t get separated from him in the bustling, frantic crowds! Just one small thing you can do to add value and make them feel more comfortable.
Sorry the spa pass is so expensive. Is there any way to ask the spa owner if you might get a bulk discount on passes? It’s too bad you make so little on the rooms…thinking it over, I revise my former opinion. I believe now that 4800 ¥ compared to a hotel is reasonable. So the shower is down the street…at least they have one!!
.But seriously what do travelers expect at that rate! I’d stay with you next time… Then I wouldn’t have to leave the capsule at ten sharp! 