Eric, I cannot say exactly why you are seeing these performance issues; there is not enough information here to go on. But I can tell you that there are a lot of layers in your stack, many of which are fairly new and not in a released state. So I would start by trying to narrow down the list of possible culprits.
For starters, unless your project requires the node.js API I would eliminate nodyn from the stack as it is arguably the most immature of the technologies you are working with. No doubt, it does make using various libraries easier. But I'm pretty sure PEG.js doesn't require any of the Node.js API. You could easily replace the entire nodyn/vertx section of the stack with a single JS file that knows how to deal with NPM modules.
Take a look at https://github.com/nodyn/jvm-npm which you can load in your top level .js file and subsequently have access to NPM packages. To be clear, this doesn't pull in any of the node.js API, but if your project is pure JS then that's OK.
load('./jvm-npm.js');
var peg = require('pegjs');
Next, I would ensure that you are using the latest dynjs snapshot which you can find here: https://oss.sonatype.org/content/repositories/snapshots/org/dynjs/dynjs/. You don't mention what version you are using, but there is ongoing development with dynjs dealing specifically with performance issues. There are some known concerns about how strings are currently handled. If you are using 0.2.2 you may find some relief in the 0.3.0-SNAPSHOT version that is currently available and updated with each new commit.
Finally, for a possible fix and more eyeball time from the core dynjs team, create a simple reproducible example, your best bet is to submit it to https://github.com/dynjs/dynjs/issues. We don't typically monitor Stack Overflow since there's not even a 1.0 release yet (although maybe we should start....). We are very active on IRC in #dynjs and #nodyn, so you might also consider spending some time there chatting with the core team about what you are seeing. We're a pretty open bunch and welcome input from our nascent user base!
charCodeAtorsubstris taking 100ms? If not, please clarify your Question.