hey there!
first off, hang in there - you are doing a great job and a hard job!
our los are now three but we have had them bw'ed since almost birth and but for growth spurts/illness/teeth they are fantastic sleepers.
i would suggest this; start by working on the 40 minute nap since that is the one (if you could lengthen it) that would make a big difference to the rest of the day. and i would say unless you intend to keep them separated, you might as well keep them in the same room. we have gone through stages of 2-3 weeks at a time where i would think they needed to be in different rooms, but they always get past it and learning to sleep in the same room is just so much easier long term....start as you mean to go on.....
so i would tackle it like this:
decide what your wind down routine is.....firm it up in your mind but make it short. i didn't 'rock' my babies at sleep time, i just hugged, kissed, put them down saying 'it's time for sleeping' as i closed the blind and then 'have a good sleep, i love you'. my friend with twins would stand by her lo's cribs and rock them in her arms for about 30 seconds while she sang a little song, then put them down. something short, because you have to do it double as you move forward. then pull the cribs closer together (i know, counter-intuitive in some ways, but it actually helps because they aren't upset when you go to comfort the other because they can still see you). put a stool in the middle so you can reach both and instead of pu/pd, sssshhhh and pat if that works. or gently lay a hand on each of them from your stool, but don't make eye contact.
see if you can get that first nap sorted and have them sleeping longer - keep them sleeping in the stroller for the second nap until you sort the first one. once you are facing a change in nap two, nap one will have them rested and they won't be going into nap two changes over tired iykwim?
you can do this on your own - it will come. just look at it one nap at a time, and remember not to beat yourself up, you are doing the right things by using bw techniques. you are comforting them when they cry, so please please don't beat yourself up - it's hard work having two small babies at this stage. it does get easier..
if you are open to it, would you consider an EASY for them? it was an amazing thing for our babies - still is in some ways - they thrive on knowing what comes next.