For us (U.S. passports) the entry to El Salvador was only $10 per person to Migracion. All officials come to your boat immediately upon arrival and then you go to the office to check in with the club and to pay Migracion in their office on club property.
I can't answer your question about renewing your "permit" since I don't know what kind of a permit you need. We did not require an agent in El Salvador or Honduras for checking in/out of those countries. I understand Guatemala is a much more expensive process, as is Nicaragua.
Please include your email address, if you need additional information.
Thanks for contacting us,
Linda and John