the over cc conversion you talk about is the transplant ka? because I know if you keep the original block while boring and stroking it don't need to go to JPJ/puspakom.
If i drive an EVO or Subaru which is modded kau kau wan. JPJ can tahan ah ? eg like big muffler, big intercooler, wastergate, BOVs, meters or gauges and big GT wings. Will they tell u to go Puspakom ?