hi rhapsody, in your examples of 2-syllable words the "stress" falls on the first syllable, as is the case for most 2-syllable latin words. (i've got a list of exceptions in a latin phonology .pdf on a temporary website http://iliad.envy.nu/
the length of the 2nd syllable doesn't affect that.
if it sounds a bit weird to u, stressing the 1st short syllable and having the 2nd long syllable unstressed, remember that (a) the stress was also a pitch
accent back then: so the word drops in pitch quite naturally from the 1st syllable into the 2nd long syllable, and (b) often in normal pronunciation romans would shorten the 2nd syllable (it's called brevis brevians, or iambic shortening), maybe so that they wouldn't sound like donkeys or something when pronouncing disyllables
i've just decided to take up latin again, and so i'm going to go through and scan and put in the accents in virgil book 2 lines 13 and ff, horace, and catullus, and then put them into readable "music lines" like i've done for greek on that website above. but for latin i can only imagine having 3 pitch levels given the way the accent works... i'll put something on that website soon once i've read a bit more. hope this helps