Sutta Reference, perception, judgment I'm looking for two suttas: 

(1) a sutta in which the Buddha says, I believe, that one is able to perceive the beautiful as ugly and the ugly as beautiful, along with other pairs that one can perceive in the way opposite to what is natural. 

(2) A sutta in which the Buddha says that you shouldn't judge others since only he or one like him knows the full extent of people's kamma. I believe it is from the long discourses.
(1) a sutta in which the Buddha says, I believe, that one is able to perceive the beautiful as ugly and the ugly as beautiful, along with other pairs that one can perceive in the way opposite to what is natural.


I am not sure if there is Sutta which mentions this but the following does have something like what you mentioned above which is called the 5 perception (pañca saññā) which appear in Metta,sahagata Sutta (quotation below), Indriya Bhāvanā Sutta, Tikandaki Sutta, etc.


  
    (1) If he wishes thus, ‘May I dwell perceiving the repulsive in the unrepulsive,’ he dwells perceiving
    the repulsive therein.
    (2) If he wishes thus, ‘May I dwell perceiving the unrepulsive in the repulsive,’ he dwells perceiving
    the unrepulsive therein.
    (3) If he wishes thus, ‘May I dwell perceiving the repulsive in the unrepulsive and in the repulsive,’
    he dwells perceiving the repulsive therein.
    (4) If he wishes thus, ‘May I dwell perceiving the unrepulsive in the repulsive and in the unrepulsive,’
    he dwells perceiving the unrepulsive therein.
    (5) If he wishes thus, ‘May I dwell rejecting both the unrepulsive and the repulsive, and dwell in
    equanimity, mindful and fully aware,’ he dwells therein equanimously, mindful and fully aware.
  





  (2) A sutta in which the Buddha says that you shouldn't judge others since only he or one like him knows the full extent of people's kamma. I believe it is from the long discourses.


Acinteyya Sutta mentions karmma is unfathomable thence thinking and trying to read too much into it is futile for a person who is not a Buddha. I think what is said is that you should not judge the working of Karma.


  
    The result of karma, bhikshus,
    is unthinkable [beyond thought], should not be thought about,
    thinking about which would bring one a share of madness or vexation.
  


Following are some Suttas which mentions judging other: 


Cūḷa Puṇṇama Sutta - Judge a true or false person
Thāna Sutta - How to truly know a person’s character