I have done this successfully before. Because you are having issues, I would NOT recommend using the migration tool to move the ruleset. Instead:
1. Download the ruleset files from 5.3
2. The 5.3 tcode-permission file, which defines which tcode permissions from SU24 need to be checked during risk analysis, needs to be split into the two files you mention above in red.
- FUNCTION_ACTION : this file represents S_TCODE objects and TCD fields mapped to each function (Function to Tcode relationship). In the 5.3 file, you will filter on object S_TCODE and field TCD, and you will get a complete list that now represents "FUNCTION_ACTION". BUT instead of having all the jumbled permission info, you will just have 3 columns: Function - Tcode - Status.
3. The remaining permissions that are left over, after taking out the S_TCODE -TCD items, represent the "FUNCTION_PERMISSION" file in GRC 10.
4. Manually create the excel spreadsheets for each file.
5. Copy and past each sheet to a unique .txt file.
6. Upload the ruleset manually through SPRO-->GRC-->Access Control-->Access Risk Analysis-->SoD Rules-->Upload SoD Rules.
7. Select each file and then upload to the correct Logical Group.
This is a huge pain, but it works. Let me know how this goes and if you need any assistance.
-Ken