I would opt for an oral assessment that can would demonstrate these skills and choose words that are used in the students' culture as well as the discipline.
I don't understand the question. Are you talking about 'assessment' of performance or about approaches to teaching stress and intonation? These would be different matters.
Himdad: If you’re interested in assessing learners’ perception, I published a test diagnosing comprehension of English intonation for speakers of any language:
Cruz-Ferreira, M. (1989). A test for non-native comprehension of intonation in English. International Review of Applied Linguistics in Language Teaching, 27(1), 23-39. doi: 10.1515/iral.1989.27.1.23
For teaching prosody/intonation, these references may be of use to you:
Chela-Flores, B. (2003). Optimizing the teaching of English suprasegmentals. Bells - Barcelona English Language and Literature Studies, 12. Online at http://www.publicacions.ub.edu/revistes/bells12/articulos.asp?codart=31
Levis, J. M., & Pickering, L. (2004). Teaching intonation in discourse using speech visualization technology. System, 32(4), 505-524. doi: 10.1016/j.system.2004.09.009
This one doesn’t involve English, but may give you tips on teaching methodology:
De Meo, A., Vitale, M., Pettorino, M., Cutugno, F., & Origlia, A. (2013). Imitation/self-imitation in computer-assisted prosody training for Chinese learners of L2 Italian. In J. M. Levis & K. LeVelle (Eds.), Proceedings of the 4th Pronunciation in Second Language Learning and Teaching Conference, Aug. 2012 (pp. 90-100). Ames, IA: Iowa State University.
Are you asking about assessing your students' performance in assigning stress to the correct syllable and using the right tone (learners' performance) or you are looking for an assessment tool that assesses the teaching of these two skills (teachers' performance)?
I think, three sets of questioners must be distribute. Knowledge asses questioner, Attitude asses questioner and function asses questioner. Then when you analyse gathered questioners, you may get a good result.
Although I am not so clear about the question, but in the case of assessing your students' performance, it would be crucially important to conduct formative assessment "Assessment for learning". That is, the assessment should help the institution to diagnose the students' weaknesses in this concern in order for the lecturer/the school to take necessary action to help improve the students' performance in the future. My two cents only.
First, Pierrehumbert's (1980) Text-Tune association system has proved to be very helpful in assessing stress, tone and intonation patterns in utterances. Again, the TOBI transcription system will provide clues to utterances since it consists of symbolic labels on four parallel tiers in analyzing prosodic events. Thirdly, analysis with sound analyses softwares: Praat, Signalyze, SFS could also provide relevant acoustic information leading to the discovery of stress (and sometimes tone)/intonation boundaries/tiers. Finally, durational variations, frequency, amplitude (intensity measured in dBs) and pausing, all determined by instrumental analysis could equally act as inevitable clues to the determination of stress and intonational patterns in utterances.