Despite being a National priority, STEM education in Australia is in crisis. With stagnant PISA scores and rapidly declining retention rates, the mechanisms influencing these factors require imminent exploration. However, the most salient consideration affecting the success and post-compulsory continuation of Australia’s Science students is that of perceived difficulty. The scaffolding practices teachers adopt to overcome this challenge balance precariously between transitioning students across a cognitive divide and straightjacketing challenge and engagement. This paper explores the challenges faced by a novice researcher when endeavouring to investigate the complex interrelationships between engagement, persistence and scaffolding. Instead of a clearly articulated and aligned paradigm, discordant approaches, typologies and meanings became evident, emerging the need for a specialised approach. This paper addresses the challenges associated with the development and implementation of research tools designed to ingress upon a students’ cognitive and conceptual workings. This snapshot of a work-in-progress research project explores the construction of a series of tools devised to purposefully research the ill-defined and abstract constructs pertaining to scaffolding, student cognition, engagement and persistence. Through the course of the research design, a hybridised fusion of methods was synthesised which entangled existing indicators with newly innovated instruments. Initial challenges regarding conflicting terminologies, meanings and typologies became apparent, producing discordance between existing tools and the requirements of the intended research. The difficulties associated with developing novel, authentic instruments which empirically capture indicators of abstract processes and constructs are explored, dissecting the issues associated with subjective influence, credibility and validity of findings. This paper discusses the systematic approach used to overcome these challenges, birthing the development of a series of innovative assessment techniques. The purpose of this paper is to instil confidence in educational researchers to develop their own mechanisms of qualitatively assessing intangible or nebulous concepts. Procurement of purposefully synthesised instruments will inevitably transform the limitations traditionally associated with accessing ambiguous concepts through educational research.