Hello Dear,
We are a team of experts with a cumulative experience of more than 50 years in the field of embedded systems, electronics, prototyping and PCB layout. Our experts have worked on 8-bit, 16-bit and 32-bit architectures developing ultra-low power designs with complex computations. We work in Smart Meters, Wireless Technologies, Automotive and Medical.
I have checked the details of your work and discussed the same in detail with my team. We are experts in MSP430 architecture. We have IAR EWB430 (licensed) along with FET430UIF and a couple of MSP430 hardware boards. I myself have worked alot on MSP430 family. I think you are concerned about knowing the error drift any attached oscillator. With a 16-bit timer in upwards continuous mode you would get an overflow when 0xFFFF--->0x0000 and there you can increment a global variable and you can tie the 1PPS interrupt to ext0 interrupt. For you method of capturing on P1.1 I may need to look in detail.
You can contact me online for help. If you want to hire me then you can also proceed and I have the tools to test and come up with a nice working solution.
Regards
Ch