I’ve just come across this important resource – a notebook of sermons heard in Oxford in 1653-54, with notes taken by Thomas Aldersey, shortly after he matriculated at Brasenose College. The list of preachers is a bit of a who’s-who of Cromwellian Oxford, and includes such names as Thomas Cole, John Conant, Edward Reynolds, Henry Savage, John Wallis, Henry Wilkinson (Canon of Christ Church), Henry Wilkinson (Principal of Magdalen Hall), and, of course, John Owen.
The reference for the sermons by Owen is MSS. Don. f. 38-41, 75v-77v (versos only, written in reverse, on 1 John 1:3) and 115v-117v (versos only, written in reverse, on John 21:20-21).
I stumbled across this source via the GEMMS website – the Gateway to Early Modern Manuscript Sermons – which boasts a portrait of Owen on its front page.