I have a 2001 VW Beetle. We have replaced literally everything and still get an EPC light on.
Have you had the computer checked?
When engine was changed,did you get the donor motor computer,or have you had the original flashed for the donor engine,this may be your issue.
You've replaced "everything", huh? Usually a Beetle with EPC lamp on needs a brake light switch, under the dash at the brake pedal. Scanning for codes would diagnose that properly for you.
Looking for a Used Beetle in your area?
CarGurus has 9,044 nationwide Beetle listings starting at $1,500.
Search Volkswagen Beetle Questions
Volkswagen Beetle Experts