All perfect praise be to Allah, The Lord of the worlds. I testify that there is none worthy of worship except Allah and that Muhammad, sallallahu ‘alayhi wa sallam, is His slave and Messenger.
Your question includes several matters, and we shall answer them in the following points:
1) If the praying person forgetfully stands up for the third Rak‘ah without sitting for the first Tashahhud and does not realise that except after standing up straight, then he should carry on with the prayer until he finishes it and perform the prostration of forgetfulness before Tasleem. The Hanbali scholar Al-Buhooti wrote:
“If he sits for the first Tashahhud but forgets to recite it, or he does not sit for it at all and stands up, he must sit down again and recite it upon remembering it as long as he has not stood up straight (to start the third Rak‘ah). Al-Mugheerah ibn Shu‘bah reported that the Prophet, sallallahu ‘alayhi wa sallam, said, ‘If anyone of you stands after two Rak‘ahs but is not yet fully standing straight, he may sit down again, but if he has stood up fully straight, then he may not sit down, and he performs the two prostrations for forgetfulness).’ [Ahmad, Abu Daawood, and Ibn Maajah] The apparent indication of the hadeeth is that he may sit down again (and recite the Tashahhud) even if he was closer to the standing position.” [Kashshaaf Al-Qinaa’]
2) The Tashahhud after the third Rak‘ah is considered an addition to the prayer; if the praying person did so deliberately, his prayer is invalidated. If he did so out of ignorance (of the relevant ruling) or forgetfulness, it does not invalidate the prayer. The Shaafi‘i book Tuhfat Al-Muhtaaj combined with Matn Al-Minhaaj reads, “If he adds extra acts to the prayer aside from the prescribed acts of the prayer, the prayer is invalidated even if these acts are of the same nature of the prescribed acts of the prayer which are among its pillars, such as adding an extra bowing or prostration to the prayer. The prayer is invalidated unless he does so out of forgetfulness or ignorance (of the ruling in this regard).” [Summarized]
3) If a person prays by nodding, he makes his nod for the prostration lower than for the bowing to the best of his ability. The Hanbali book Daqaa’iq Uli An-Nuha reads, "If he cannot perform the bowing and the prostration, he nods to perform them and makes his prostration lower to distinguish it (from the bowing).”
As you are not sure whether you made your bowing lower than the prostration or not, in addition to suffering from Waswasah, then it is most likely that you did the right thing, and these doubts are due to Waswasah, may Allah cure you from it. For more benefit, please refer to fatwa 343948.
4) If a person frequently experiences doubts regarding the prayer on a daily basis, even if once a day, he should disregard them and not act upon them. He is not required to perform the prostration of forgetfulness in this case.
The Hanbali scholar Al-Mardaawi wrote, “Whoever frequently performs the prostration of forgetfulness until it becomes like a Waswaas (obsession), he should disregard it because it becomes a sort of stubbornness and leads to adding extra acts to the prayer despite believing with certainty that it was performed fully and the like. Therefore, he should disregard it.” [Al-'Insaaf]
5) What appears to us from the question is that your prayer is valid, and you are not required to repeat it. There is no harm in performing the prostration of forgetfulness before Tasleem all the time.
The Hanbali book Daqaa'iq Uli An-Nuha combined with Muntaha Al-'Iraadaat reads, “Whether to perform it (the prostration of forgetfulness) before or after Tasleem is a recommended matter (not obligatory) because the ahaadeeth included both manners. So if he performs the prostration for all forgetfulness before Tasleem or after it, both are permissible.”
However, we advise you to disregard Waswaas and to ignore it completely, as that is the best remedy for it.
It should be noted that every Muslim, male and female alike, is obliged to learn about the individual religious obligations such as purification, ablution, Ghusl (ritual shower), prayer, and the like of the obligatory acts of worship that Allah has enjoined on every Muslim individual.
Allah knows best.