We did have a good night last night, although I'm not sure if it's progress or just a fluke. My husband was out for the evening and I didn't think I'd be able to get both kids to bed on my own, but it worked out great! They both even had a bath! Once they were both ready I put Noah (#1 son) to bed (Simon in my arms while I sung Noah his goodnight song) and then I told Noah I'd come back to check on him after I got Simon to bed - and I told him he wouldn't be able to call out for me to come back because I just wouldn't be able to come until Simon was looked after. Simon got to sleep in about 10 mins (still using pat/sh on him after 4 months, but that's another story...) and there was not a single peep out of Noah! I went back to his room as promised and he was awake, so I told him how proud I was that he was so quiet, and that if he could be just as quiet until he went to sleep he would get a sticker in the morning (DH bought him some special bedtime stickers that until now hadn't worked). Much to my surprise, Noah went to sleep without another sound. It was like heaven - and it's been a very long time since he went to sleep that well.
So here's what I learned from all that...maybe some of Noah's issues have centered around the fact that we've been putting the kids to bed separately - one parent with each child, just like you - and it might have been causing some jealously issues. Last night, Simon and Noah were together the whole time as got each of them through their bedtime routines, and I think that made Noah feel like he wasn't missing out on anything. Secondly, because I was doing it all myself, Noah got to bed about 15 minutes later than usual, and that might have been just enough extra time to get him a little more tired.
Tonight I'll try doing their bedtime stuff together again, and maybe even bath them together since Simon is sitting up pretty well now.
Sorry for the long post but I hope it will help. It's interesting our kids are almost exactly the same ages and we're having the same problem!