It seems that RegionFrii is bugged (because the offset of the third partition is bigger than 0xFFFFFFFF). So extracted partitions #2 and #3 are not the good ones.
With WiiBrowse, partition #3 can be extracted but partition #2 can't be extracted, because his size is bigger than 2 Gb (an another bug ...
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You can try this way to remove the #001 in the third partition. Not tested yet.
1. With WiiBrowse, extract the #3 partition of MKW iso in encoded format (.enc)
2. With RegionFree, inject this enc file in the first partition of an other two-partition iso.
3. With Trucha, open the two-partition iso and extract the mail.dol of the first partition.
4. With GWP path the main.dol to remove the #001 error.
5. With Trucha, replace the mail.dol of the first partition with the patched file and sign the partition to patch the iso.
6. With WiiBrowse, extract the #1 partition of the patched iso in encoded format (*.enc)
7. With an hexadecimal editor, open the MKW iso, go to offset 0x01155D0000 and replace the 31'588'352 following bytes with those of your generated enc file.
I hope it works.