Cap states dot3 which has been replaced with dot4, i'm guessing that's what's in there now, will I have any problems just replacing with dot 4 or even dot 5.1 ?

Or do I need to flush out with anything 1st, last thing I want to do is rot the insides of my system

I have shell dot 5.1 in mine, Seems to be ok.

Dot 5.1 will give higher tolerance to heat and any moisture ingress. Used the shell product for years on bikes and cars would recommend it