If i join jamaat salat at the secor second rakaat of Ishaa when the imam is in qunoot, and i have not yet prayed maghrib, can i join with niyat of jamat ishaa or maghrib ? If it is niyat of maghrib, then will it be my first rakaat of maghrib while its the imam’s second rakaat of ishaa? If so, if i don’t have enough time to complete recitation of surah fateha and Qul but i am able to go in ruku with imam, is this salaat valid? Finally, in this case if i dont have enough time to complete surah fateha and qul but the imam is in qunoot, am i supposed to raise my hands in qunoot even if its my first rakaat?

Yes it is isha of Imam but yields have to follow the order of the namaz first make niyat of the maghrib for Jamat and it will be considered as your first rakat if surah were missed still you are able to attend either in qunoot or ruku as it was mentioned that it is second rakat
Recite the qunoot with the intention to get the thawab but it is your first rakat at the time of tashhud again sit with Imam and people and read for thawab then when Imam pray his third rakat it is your second try to recite both surah if not possible minimum read sura Fatiha and do small qunoot to make sure to get Imam in ruku after sajda imam will stand for his fourth and you read your tashhahud then stand pray your third rakat with jamat while it is their fourth and finish your prayer with Imam and jamat