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Were the stigmata wounds just on the skin or did it go deeper in the hands and feet?

He allowed my painful studies by doctors over his life time--the wounds, which he had for 50 years, went all the way through his hands and feet and would only bleed during the Consecration. The rest of the time, they'd scab over. But considering he offered Mass Daily, his wounds bled daily.

The crazy thing was that after he died, his hands completely healed with not even a scar (from what I read in his biographies).

I would love to go to see his body in a few months, but there's little chance I'll be able to do that.

Were the stigmata wounds just on the skin or did it go deeper in the hands and feet?

According to the link posted above,

P. Pio writing to P. Benedetto little more than a month afterwards: "It all happened in a flash. While all this was taking place, I saw before me a mysterious Person, similar to the one I had seen on August 5th, differing only because His hands, feet and side were dripping blood. The sight of Him frightened me: what I felt at that moment is indescribable. 'I thought I would die, and would have died if the Lord hadn't intervened and strengthened my heart which was about to burst out of my chest. The Person disappeared and I became aware that my hands, feet and side were pierced and were dripping with blood" (Ep., V. 1, no. 5 10, p. 1094). P. Pio had just received the visible stigmata. There was nobody about. Silence settled once more round the brown robed figure now lying huddled on the floor.

The information at the above link also provides his reaction:

He had not desired this physical conformity and when he had recovered somewhat from the immediate experience his embarrassment was extreme: "I am dying of pain because of the wound and because of the resulting embarrassment which I feel deep within my soul. . . Will Jesus who is so good grant me this grace ? Will he at least relieve me of the embarrassment which these outward signs cause me" (Ep., V. 1, p. 1904). Not the wound, not the pain did he wish removed but only the visible signs which at the time he considered to be an indescribable and almost unbearable humiliation.
Later, much later, however, he would come to love and cherish these divine marks of predilection, drawing from them that rich source of superhuman energy which from then on marked his apostolate of love and suffering. With Catherine of Siena he could truly say: "My wounds not only do not afflict my body, but they sustain and fortify it. I feel that what formerly depressed me, now invigorates me." His wounds, hitherto invisible but now manifested exteriorly, mark a definitive stage of his soul's transformation into the object loved, namely, the Lord who suffered and was crucified.
For the next fifty years they would confound impartial science; their continuous and profuse effusion of blood, accompanied often by the sweetest fragrance, came to be regarded as a prolonged miracle, because, as the experts correctly state, blood for its production requires nourishment while this friar's extraordinary frugality was such as hardly to maintain the life of a small child.
The remarkable nature of this miraculous gift becomes more apparent when it is considered how such loss of blood was simply inconsonant with and disproportionate to the stamina and energy with which P. Pio with ever greater activity and zeal conducted his life in all matters relating to the service of God.

Not surprisingly, on the exhumed body of St. Pio, there is no sign of the stigmata. This is not surprising to Catholics. We are accustomed to the stories of saints who have asked our Lord, with a sincere heart, for a share in His Passion.

St. Rafqa, a Maronite Lebanese Catholic nun was born on June 29, 1832 and was given the name Petronilla as a reminder that she was a daughter of St. Peter, on whose feast day she entered the world. On the first sunday of October 1885, she entered the convent church and began to pray, asking God to make her a part of his divine pains. God responded immediately. Unbearable pains began in her head and moved to her eyes. All attempts to cure her failed. It was decided to send her to Beirut to receive treatment. She passed by St. John-Marc's church in Byblos, where an American doctor examined her. During the surgery, he accidentally pulled out her right eye. Then the disease spread to the left eye, and the doctors considered the treatment useless. After all that, she returned to her monastery where she suffered from terrible pains in her eyes for 12 years. She remained patient, silent, praying in joy sharing the pains of Jesus.