Hello… 
When a monk commits a thullaccaya offense, What should be done to fix it? 
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Do I understand correctly that, as stated in the above linked text, a bhikkhu eating human flesh is a lesser offence than touching the edge of a woman’s dress? 
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It depends on which type of offense the thullaccaya offense commited relates to.
To understand that one will need a Vinaya expert who will use both the vibhanga texts, the commentaries and his judgement/ inference to inform the offender and the rest of the community involved of what is applicable.
The link below may be of help:
“Rules entailing thullaccaya offenses are found in the Sutta Vibhaṅga as derivatives from pārājika and saṅghādisesa rules; in the Khandhakas, as stand-alone rules.
The fact that they are scattered throughout the Canon with no special arrangement or section of their own makes it difficult to determine whether one has committed an offense of this class.
To lessen this difficulty, they are gathered here. For thullaccayas in the Sutta Vibhaṅga, I have provided summaries in my own words. For those in the Khandhakas, I have given the rules in their original form, arranging them in the order in which they are found in BMC2.”
Appendices | The Buddhist Monastic Code, Volumes I & II
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Thullacayas are derived offenses and some Vinaya experts Ive heard suggest that as they are not in the patimokkha itself they are much later additions. They are often behaviour leading toward the more serious offences of pārājika and sanghādisesa, like open mouth kissing, which could get a monk or nun in a bit of trouble… So acknowledging it is important for us to do. This is done through either a specific or general confession to another monastic usually before a patimokkha.
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Hmm… Example he committed to have a surgery on his male organ or cut his male organ, how to fix the offence? 
He better ask the relevant Vinaya expert in his local monastic community.
I am no monastic and no Vinaya expert.
Rules often have origin stores that explain why they came to be. For example, consider if someone maddened by sexual desire castrated oneself. That would be a very violent and self-abusive act then and now. Self-abuse is an aspect of mortification. Surgery for testicular cancer is different. Much hinges on the intent.
As Gnlaera mentioned, the particular details would have to come from a Vinaya expert. You can however, explore Vinaya origin stories yourself to get a sense of how the rules arise. It is quite interesting reading.
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It’s difficult to find a monk in Indonesia who expert in Vinaya. 
As I know when a monk commited a Sanghadisesa, he must go to Thailand to rehabilitate. Cz it’s almost impossible to find 20 monks in one place until his rehabilitation done. As I know that Thullaccaya is quite big case too, how to fix the offence? 
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Normal confession procedure, just as in paccittiya.
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After he confess his offence, the problem is solved? Did he get no punishment?
Ajahn Brahm has preforgiven any and everything unskilful we will ever do. He recommends we do likewise. Acknowledge, forgive, learn - that sounds a bit like Buddhism but I could be wrong? 
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When I tell the teacher that I remember 1+1=3 does punishment help?
Punishment takes us out of present awareness and drowns us in remorse in the past.
In that drowning of remorse and regret enforced by punishment we perpetuate the offense of lack of clear and present awareness. Putting a murderer in jail doesn’t bring back a loved one–it merely prevents the murderer from murdering people not in prison. Confined so, the murderer might reconsider or might not.
When I listen to a sutta and my thoughts wander about should I punish myself or should I simply take note of my transgression and then return to awareness?
Sometimes punishment can help or even be necessary to let go of guilt, or seeds of ill will & resentment.
But it might take an unusual sort of person to give such a gift without risk or harm to any.
Perhaps it is extremely difficult to receive that except with clarity, discipline, even ritual, without potential for harm to any touched by it.
Perhaps those who live in robes might find this in sangha.
May all be happy, peaceful, freed from suffering.
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Where it gets tricky is that there comes a notion of “balance” and “repayment”. With the accountant perspective of punishment, we somehow wander into capital punishment as a means to “right” a “wrong”. And people think this is “fair”, that death should repay death.
Yet the Buddha did not repay death with death. All he said to Aṅgulimāla was:
I’ve stopped, Aṅgulimāla—now you stop –MN86
There was no punishment. Aṅgulimāla went forth and the people threw things at him to hurt him. The Buddha told him that was his kamma. The Buddha did not say it was his punishment.
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Yes no problem. The problem is not what happened, but to live free of shame and guilt, and fear, and self-contempt.
These rules are not to punish but support the practice of a monk; they’re carried out sensibly and compassionately. Monk’s not a child!
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@karl_lew 
Agree.
Imo, fairness and justice are delusions; they seem to involve POVs which involve belief in a self or soul, as well as an odd view of time (static assessment or perception, but some external infinite reality? Just a mental fabrication as far as I can understand at this time.)
Transactional relationships tend be problematic also, as I see things, even transactional relationship with the universe IF seen as “personal”. It really doesn’t seem (to me) to be how it is. Kamma doesn’t seem (to me) to be fair, or personal, or Just; it just is what it is, or how it goes…
How fortunate Aṅgulimāla was; how fortunate are we, to have that wonderful lesson(s) in that anecdote!
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I doubt that expertise…
It is not correct to take pathimokka as the basic vinaya where there are more important rules in kandhakas. Earliest texts for vinaya are parajikapali, pacittiyapali and kandhakas. Pathimokka was created later to conduct uposatas. However, there are hundreds of rules in cullavagga, that we cannot find in patimokka.