My copy of FSX shows SPJC for Jorge Chavez International Lima, but I updated to AIRAC cycle 2112 using fsAerodata; this gave me consistency across SimBrief, FSX and PF3. Unfortunately the fsAerodata service closed in January 2022, so this option is no longer available.
I think that you have two options:
1) Plan your flight using SimBrief, and then edit the flight plan to change SPJC to SPIM (as you already said).
This is probably the simplest option and will make the plan usable with PF3 and FSX.
2) Edit the CSV files produced by MakeRwys to change all references to SPIM to SPJC, and then reload the PF3 database.
This will fix the issue for PF3, but means that FSX wouldn't understand the flight plan (so aircraft GPS wouldn't work, for instance).
Hope this helps,
Martin