Have you written the scenes for all those events already? Or are you still in the outlining stage for the middle/end?
I'm not sure that Dramatica can help very much with the disconnectedness. It may just be the hard work you have to do to figure out how things tie together... It may be easier than you think, because following a storyform will have kept them all "connectable" (it's like you only used real Lego, no knock-offs that don't connect).
Have you tried something like this? Take the ones you want to keep (the ones you really want to write, or at least want to be in the story) and draw them in boxes on a large piece of paper. Looking at them like that, your muse will immediately start offering connections. Some might be as easy as drawing arrows because they connect obviously. For others you can add in new boxes that will allow connections to make sense.
Like this (I would use paper but googled and found sketchboard.me, pretty cool):
The blue is something new I added to brainstorm a connection. It might not have the right Driver but you get the idea.
When laid out like you'll hopefully find your muse offering suggestions for connections. I'm staring at the gas plant and Mike kills nodes and thinking, does someone learn about Mike's past at the gas plant? Does one of the employees there know him? Or maybe Mike convinces the others to blow the gas plant in order to kill someone who works there? etc.
When doing this do NOT worry about the storyform, just let your muse suggest things and write down the ones you like, and/or ask yourself further questions about them, writing down the questions and answers as needed. Judge ideas based on coolness and gut feel. The storyform alignment can be adjusted later (though you'll probably find it's there already if something seems cool).
Also, don't worry about "rules" in terms of story-weaving. If something happens in the MC throughline that sets up something in the OS, or whatever, that's totally fine. At the level of logically connecting events in the story, you're supposed to be weaving the throughlines together. (e.g. in my story the MC has an argument with his dad in the car and his dad leaves him by the side of the road (MC throughline), which makes him late to meet the IC and deliver a warning message to her, so she ends up getting abducted by her alien-controlled professor, which is super important for both IC and OS throughlines.)