Using window.setTimeout() and window.setInterval() in this situation

Question 1

If I understood correctly and you're trying to support multiple charts updating concurrently, I'd switch from keeping the chart data inside the connectToVM() closure to an explicit array of chart objects and use a single interval to update all charts.

Something like the following (treat it as pseudo-code):

var charts = [
  // an array of chart objects, see addChart()
];

function addChart() {
  // when you need to add or remove a chart, update the charts object, like this:
  charts.push({
    update: updateChart,
    nextUpdateTime: null, // or Date.now() if you don't care about old browsers.
    chartData: {host: ..., port: ..., user: ..., passwd: ..., db: ...,
                originalTitle: ..., portalId: ...},
  });
  restartUpdates();
}

var activeInterval = null;
function restartUpdates() {
  if (activeInterval) {
    clearInterval(activeInterval);
  }
  activeInterval = setInterval(updateCharts, 5000);
}

// updates all active charts
function updateCharts() {
  var now = new Date().getTime();
  for (var i = 0; i < charts.length; i++) {
    var chart = charts[i];
    if (chart.nextUpdateTime !== null && chart.nextUpdateTime < now) {
      chart.nextUpdateTime = null; // chart.update() will re-set this
      try {
        chart.update(chart);
      } catch(e) {
        // handle the error
      }
    }
  }

// update a single chart.
// @param |chart| is an item from the |charts| array.
function updateChart(chart) {
  // ...same as your connectToVM() using properties from chart.chartData...
  Ext.Ajax.request(
    // ...
      success: function (response, options) {
        // ...same as before...
        // ...but instead of re-setting the timeout:
        //   windowInterval = window.setTimeout(function() {
        //       connectToVM(portalId, host, port, user, passwd, db)
        //     }
        //   , 4000);
        // ...update the chart's nextUpdateTime:
        chart.nextUpdateTime = (new Date().getTime()) + 4000;
      }
  );
}

initial answer below

Thanks for the detailed question! It feels you're missing something very obvious wrt questions #2/3, but it's hard to tell what specifically without seeing more of your code. Can you post a more complete, yes simple example demonstrating the problem you're trying to solve? Perhaps the function handling changing the active tab in pseudocode would help, like this:

function selectTab(tabID) {
  // ...activate tab #tabID in the GUI...
  if (tabID == 1) {
    // there's chart #1 on tab #1, need to stop any active timeouts and start a new one 
    connectToVM("chart #1");
  } else if (tabID == 2) {
    // no charts on tab #2.. need to stop any active timeouts
  } else if (tabID == 3) {
    // ...
  }
}

One thing I don't understand is whether there's always a single chart, that needs updating, at any point of time?

Also, do you know the concepts mentioned in A re-introduction to JavaScript, specifically objects?

As for the questions:

1: yes, too many timeouts should be avoided (thousands a second will probably make the CPU hot and the browser sluggish), although I'd be more worried about the server, which has to handle the requests from multiple clients.
2/3: see above.
4: The Comet page lists a lot of alternatives to basic AJAX polling (server-sent events, long-polling, websockets), but I'd worry about this later.

Question 2

Yes
var x = window.setTimeout(...); window.clearTimeout(x);
Store it as a data attribute on the active tab, a property on your object, or as a global variable. Many different ways. Example code would have made it easier to answer this.

Based on your comments:

var windowInterval;
function connectToVM(portal) {
    if(windowInterval)window.clearTimeout(windowInterval);
    windowInterval = window.setTimeout(function() { ... }, 4000);
}