Warning, I don't know this case. Looking at it online, it looks somewhat like an Obsidian 900D.
If you are looking to get rid of your optical bays, and are ok with the idea of drilling out any cages etc, then I would say that your plan seems sound - but I don't know for sure.
If it were me, I would do one of two things, depending upon my budget/desire to work harder for what I want etc.
1) Research and invest in a case which requires less modding/provides more of what I am after out of the box. Fractal Cases are my personal favourite, with the Define S and C being especially good choices, if you are looking to have a smaller rig footprint. In any event, be prepared to do a LOT of looking at cases online and research.
2) If you are happy with the case, and are dead-set on modding it, plan out the set up very carefully, and test at every point that you are not compromising the strength of the case (this is the tricky part actually).
I have recently been going through and doing some test take aparts of some other cases (in prep for my project), and the number of times that they go back together with less strength (because of bolts instead of rivets for instance) is amazing [as an aside: I totally have to get a rivnut gun].
Whatever you decide, I look forward to seeing what you build, so would encourage a build log. There is a lot of flack levelled at Thermaltake here (sometimes), and whilst it is justified (case idea theft for instance, poor quality case builds sometimes), you have to try to remember it isn't personal. I too used to have a Thermaltake case, and have found that there are much better cases, for less, for what I do. Personally, I'd love to see Thermaltake send Tom a review sample of one of their cases (caveat: it has to be full of their OWN ideas), and just see what he says about it.
Just my 2 cents.