There are bigger improvements you can do that will go a longer way with comfort if you're actually typing that much. I think getting a comfortable ergonomic chair (I prefer Herman Miller) and a desk that's at a proper height will help your comfort far more than getting different key switches. But if you're content with your desk and chair setup or if those are out of your control, then there are other small improvements that you can make. I got a large desk mat that my keyboard and mouse sit on and that has helped further dampen my key strokes. Small comfort but I don't like to type long term without it now.
As for key switches for comfort, I found that getting my HHKB, which is lubed and hypersphere'd, did help my comfort levels.The key switches far smoother than my cherry-browns and my Novatouch (NVT does not feel like Topre to me). I've since sold them. I think the thing about Topre is that it's very smooth and it feels very consistent. It's probably more of a preference though. I definitely took a chance with the HHKB because I had no opportunity to test it first. I just figured that at worst, I could sell it with minimal loss.
If it's difficult to acquire a Topre board, you could also adjust your current board like adjusting the height, or adjusting your keycaps (switching from OEM profile to cherry profile made a difference for me, I like the lower height).
Another thing I feel is that if you're coming from a full-size, getting a smaller keyboard helps because your body will be in a more neutral position when using the keyboard plus the mouse. I can't quite use full-sized keyboards anymore because it forces me to sit a bit awkwardly. I also try to use my keyboard as much as possible (I've switched to using VIM in XCode) which has also helped a bit.