I often have coffee & cake/cookies together, say both pre-Brachot, but finish the Mezonot quite quickly and enjoy finishing the coffee perhaps later while working. I thus wonder whether I should say "Al-Hamichya" after finishing the Mezonot (in case I forget later?); or should I consider it a mini-meal and wait until the coffee is also finished before making both after-Brachot?

If there is a chance you will forget the Bracha say it then and there (see Shulchan Aruch OC 178,2 and Mishnah Brurah ibid 36)