How to trace per-file IO operations in Linux?

You could wait for the files to be opened so you can learn the fd and attach strace after the process launch like this:

strace -p pid -e trace=file -e read=fd

First, you probably don't need to keep track because mapping between fd and path is available in /proc/PID/fd/.

Second, maybe you should use the LD_PRELOAD trick and overload in C open, seek and read system call. There are some article here and there about how to overload malloc/free.

I guess it won't be too different to apply the same kind of trick for those system calls. It needs to be implemented in C, but it should take far less code and be more precise than parsing strace output.