I would suggest you to
Create a MyCase (Top of this page-> Design Support -> Create a Support Case)
and / or contact your local Cypress representative.
Nice work! My current version of that machine is me and a grad student and our shaky coffee fueled hands which makes for slow progress.
Do you offer PSoC programming as a service?
We started that way too but our fingers started hurting and got shaky too which wasn't good for the tiny pins.
I've made the programming software myself and it's also possible to have serial numbering inside EEPROM.
I can offer it as service, feel free to contact me at: rolf (at) nooteboom.biz