My understanding is Interrupts interrupt software based serial routines like Serin2 and break them..
Have I missed something? I can't use hardware serial in this application due to pinout constraints
no , thats pretty right any software timed function is compromised

if you use an asm timer interrupt to set a flag to be processed in main code when needed and your serial baud rate is not too high
you may get away with it. i would use define int rather than dt ints to minimise overheads

another option is to disable the int when serial transactions are being carried out

better still use a modern chip like k42 series with peripheral pin management , nearly any pin can be any function
and they have 2 esuarts

this ticker , what sort of range does it need , i tend to use a 4mS timer counting a 16 bit counter , allows me to measure
65535x4mS periods a 4 minute-ish rollover