i would contact animal health once you know the CPH number and advise them of the pigs. They will issue a herd number, often over the phone with written confirmation following. Dont rely on the SGRIP getting you the herd no, as there are a lot of CPHs without herds attached, they will p[rob just advise the CPH no and thats it.
You will need a herd no for each species of farm animal you keep (sheep, goats,cattle, pigs etc) but often they will allow you to have the same herd no across species, BUT you have to still advise them every time you start keeping or stop keeping one of the species (so they can start/stop sending you the relevant docs and for disease monitoring).
I dont quite understand the 'estate' maps bit, the CPH will be covering land which is identified using the latest Ordnance survey map, and they dont miss stuff out, far from it, even our high fence within a field is shown in the latest one! And ownership is not that relevant as you could have been a tenant farmer, they could still be the farmer and have the CPH/herd no, so I dont think that matters so much, altho maybe it does when it comes to claiming subsidies and grants (we dont claim any so doesnt affect us)
Should add we are in Scotland too, currently only have sheep but did previously have cattle and sheep.