Basically, each kernel has its own modules.
If you recompile the same kernel version as TC's (2.6.29), the modules are alright, you can keep them. However, if you change it with a newer/older kernel, make sure to remaster TC with the right modules, because the extensions won't work with a different kernel.
By the way, if you replace the kernel, you may face other problems, because the toolchain (the C library, specifically) is compiled against the kernel headers, and may be incompatible with the newer kernel. It depends on the way TC is built ... in my distro I compiled the C library for the latest (2.6.31.6) kernel headers without support for older kernels. If TC is built this way, you shouldn't replace the kernel, the maximum you can do is replacing the 2.6.29.x TC has with the latest 2.6.29.x release (each 2.6.Y has its own headers).
My suggestion: stick with defaults. TC does not stand for "Turbo Charged|, TC is not meant to be super-optimized or something ... that's why it's i486 with i686 optimizations and not just i686. If you really want TC to be like that, you can rebuild it with your own, manually compiled binaries.