The OP's question asks "where was Jesus" after He stopped breathing on the cross.
this presents a problem because "death" seems to be quite common among mankind as shown beginning in Gen 5:5:
And all the days that Adam lived were nine hundred and thirty years: and he died.
And all the days of Seth were nine hundred and twelve years: and he died.
On and on throughout Scripture, all those who in the past have believed in the good news that the Lord God gave to Eve after man's sin have died. All these were listed in Scripture as being Saints long before Jesus Christ was manifest in the flesh as the Son of man/Son of God. Each and every one of the believers were anxiously awaiting the "seed of the woman" promised to Eve to come and to redeem them, even after their eminent future deaths.
THEN, we are more fully informed about this great faith in the promise of the WORD of God, and of the death that we are so curious about, in Genesis 25:8:
Then Abraham gave up the ghost, and died in a good old age, an old man, and full of years; and was gathered to his people. (My emphasis)
Again, Gen 35:29:
And Isaac gave up the ghost, and died, and was gathered unto his people, being old and full of days: and his sons Esau and Jacob buried him. (My emphasis)
So the death of Abraham and Isaac consisted of their ghost being given up --separated-- from their bodies and those bodies were both buried after they gave up the ghost and died. So, what exactly was gathered to their people, and who were their people? Job brings to light quite a bit about this when he speaks of his own death together with his faith in his redeemer in Job 19:25-27:
For I know that my redeemer liveth, and that he shall stand at the latter day upon the earth: And though after my skin worms destroy this body, yet in my flesh shall I see God: Whom I shall see for myself, and mine eyes shall behold, and not another; though my reins be consumed within me. (My emphasis)
Without question, Job is expecting a bodily resurrection here. Moreover, Job also speaks of the the difference between people like himself who have faith in the WORD of God--that seed of the woman, and the unbelievers scheduled for judgment in Job 19:25-29:
But ye should say, Why persecute we him, seeing the root of the matter is found in me? Be ye afraid of the sword: for wrath bringeth the punishments of the sword, that ye may know there is a judgment.
So there are two categories of human dead, believers in the seed of the woman, and unbelievers. That seed was promised to come through Abraham by the promise of the WORD of God. That seed was not a large body of Abraham's physical sons, but rather the promise of one son, Jesus Christ, as shown in Galtians 3:15-18:
Brethren, I speak after the manner of men; Though it be but a man's covenant, yet if it be confirmed, no man disannulleth, or addeth thereto. Now to Abraham and his seed were the promises made. He saith not, And to seeds, as of many; but as of one, And to thy seed, which is Christ. And this I say, that the covenant, that was confirmed before of God in Christ, the law, which was four hundred and thirty years after, cannot disannul, that it should make the promise of none effect. For if the inheritance be of the law, it is no more of promise: but God gave it to Abraham by promise. (My emphasis)
THEREFORE, it is appropriate that the term, Abraham's bosom, means the confidence in God's promise to Abraham by faith, not in Abraham's physical bosom that has certainly, by now, decayed with the help of worms. Yet, Abraham was (by faith) expecting that same bodily resurrection of his body that Job (by faith) expected of his body. That promise was understood and expected to be a bodily resurrection because it included a physical death, just like Job's physical death, as we see in Genesis 15:13-15:
And he said unto Abram, Know of a surety that thy seed shall be a stranger in a land that is not theirs, and shall serve them; and they shall afflict them four hundred years; And also that nation, whom they shall serve, will I judge: and afterward shall they come out with great substance. And thou shalt go to thy fathers in peace; thou shalt be buried in a good old age.
So that one seed would come forth out of the (many) seed of Abraham--the people--nation of Israel. That one seed was later promised to that nation to be of only one particular seed of only one Jewish virgin, in Isaiah 7:13-14:
And he said, Hear ye now, O house of David; Is it a small thing for you to weary men, but will ye weary my God also? Therefore the Lord himself shall give you a sign; Behold, a virgin shall conceive, and bear a son, and shall call his name Immanuel.
That Son is Jesus Christ who was also promised to take upon Himself the sin of the world and to be put to death for that sin--not his own sin. When Jesus was put to death, His death was not unlike that of any other man, even though His Spirit was the very Spirit of God. At the time of His death, that Spirit was separated from His body just like that of Abraham and Isaac, as we see in John 19:30:
When Jesus therefore had received the vinegar, he said, It is finished: and he bowed his head, and gave up the ghost. (My emphasis)
Jesus' body was left wrapped up in a nearly grade-level tomb for three days and three nights--not in the heart of the earth. The malefactor's spirit was also separated from his body. Clearly, if Christ's body was not in heaven, but rather in a tomb, the malefactor's body could not have accelerated ahead of Jesus into heaven. Jesus' body was not in the heart of the earth. But Jesus was in the heart of the earth for those next three days and three nights, according to Jesus--not known to be a liar--in Matthew 12:39-40:
But he answered and said unto them, An evil and adulterous generation seeketh after a sign; and there shall no sign be given to it, but the sign of the prophet Jonas: For as Jonas was three days and three nights in the whale's belly; so shall the Son of man be three days and three nights in the heart of the earth. (My emphasis)
1 Peter 3:18-19 reveals:
For Christ also hath once suffered for sins, the just for the unjust, that he might bring us to God, being put to death in the flesh, but quickened by the Spirit: By which also he went and preached unto the spirits in prison;
This clearly shows the separation of the Spirit from the flesh, because, those spirits who Jesus preached to could not have been in heaven, or there would have been no need for Jesus to preach to them. They were in Abraham's bosom in the heart of the earth--Hades-- while awaiting the good news of their Salvation to be fulfilled by that seed of the woman, Jesus Christ. Jesus was preaching to them that their faith in the sacrificial death of the seed of the woman was not in vain. It had already happened, and that Jesus was about to lead those captive souls captive with Him to a place for them to await their bodily resurrection.
All those saints, having all these years believed the promise of God, have not yet received the FULL PROMISE-- the resurrection of their physical bodies to be enjoined with their new eternal spirit that has now been already provided them through faith. That resurrection will happen at one great event--the coming of Jesus Christ appearing to them in the clouds without sin. At that time, even all the living bodies who believe shall be changed, and the church, as a group of resurrected women, men, and children, will be MADE PERFECT, as we read in 1 Thessalonians 4:16-18:
For the Lord himself shall descend from heaven with a shout, with the voice of the archangel, and with the trump of God: and the dead in Christ shall rise first: Then we which are alive and remain shall be caught up together with them in the clouds, to meet the Lord in the air: and so shall we ever be with the Lord. Wherefore comfort one another with these words.
Yes, the malefactor's spirit was with Jesus that very day--in Abraham's bosom in Hell--Hades--in the heart of the earth. No, the malefactor's body was not with Jesus that day, their bodies were in different places--different tombs. In fact, all those saints bodies which were put through all kinds of torture and suffering are still waiting for that appearance Of Jesus Christ--without sin--to resurrect our bodies and take them up into heaven enjoining them with His eternal spirit, to be with Him forever, as we see in Hebrews 11:39-40:
And these all, having obtained a good report through faith, received not the promise: God having provided some better thing for us, that they without us should not be made perfect.