What is the difference between MSR and 1PPS?

There is no direct relationship between the MSR and the PPS. The 1PPS is a pulse where the leading edge is synchronized to receiver calculated GPS time. The MSR is a 1ms pulse that is synchronized with internal GNSS measurements. The MSR pulse is NOT aligned with the PPS. This is a pulse that is generated when the receiver is taking pseudorange measurements. This pulse also drives the internal tasks running within the receiver. It does not necessarily align to GPS time, and it can happen anytime within a second, multiple times a second. Therefore, if a task that needs to be synchronized to GPS time, the 1 PPS pin must be used.