Subject and Verb

Original sentence:

1. The kernel comprises a set of routines, mostly written in C, that communicate with the hardware directly.

My modified sentence:

2. The kernel comprises a set of routines, that [are/is] mostly written in C, that communicate with the hardware directly.    (What does that first 'that' refer to? Is it 'kernel' or 'set' or 'routines' ? How do you figure it out? It's so complicated!! What does the second 'that' refer to?)

Thanks!!

The way I first read it, by setting off the "mostly written in C" with the commas, you are making it additional or parenthetical information. So the kernel is the subject. And as a singular word, you need the singular verb form, communicates.

But on a second reading, I thought that perhaps routines are supposed to be the things that communicate, not the kernel.  (Perhaps your readers would know that? Kernels are things I turn into popcorn.) But as it is, the construction leads to ambiguity.  

Try one of these, depending on what the real meaning is:

The kernel comprises a set of routines mostly written in C and communicates with the hardware directly. Here the kernel comprises and communicates.

or

The kernel comprises a set of routines, which are mostly written in C and communicate with the hardware directly.  Here the routes are written in C and communite.