Just change the following line

otArr.push('"' + e + '": {' + itArr.join(',') + '}');

to

otArr.push('"' + (e+1) + '": {' + itArr.join(',') + '}');

The parenthesis will add the values as numbers not strings.

Also, add keys array for internal object keys.

function html2json() {
   var json = '{';
   var otArr = [];
  // var i = 1;
   var tbl2 = $('table tbody tr').each(function(e) {        
      x = $(this).children();
      var itArr = [];
      var keys = ['no','name','lastname'];
      x.each(function(i) {
         itArr.push('"' + keys[i] + '":"' + $(this).text() + '"');
      });
      otArr.push('"' + (e+1) + '": {' + itArr.join(',') + '}');
   })
   json += otArr.join(",") + '}'

   return json;
}

Profile both. Optimize afterwards.

There are different options for representing data in JSON (or any format).

Here is an example of one way I would choose to represent the data in the originally posted question:

{   "PHC": [{"CEP": {"Status": "Done", "Notes": "Inspector remarks here"}}],

    "PVC": [{"CFP": {"Status": "Done", "Notes": "Inspector remarks here"},
             "CIL": {"Status": "Done", "Notes": "Inspector remarks here"},
             "CLL": {"Status": "Done", "Notes": "Inspector remarks here"},
             "CPC": {"Status": "Done", "Notes": "Inspector remarks here"},
             "CPQ": {"Status": "Done", "Notes": "Inspector remarks here"},
             "CPS": {"Status": "Done", "Notes": "Inspector remarks here"},
             "CPA": {"Status": "Done", "Notes": "Inspector remarks here"}}],

    "CovTest": [{"FrontCT": {"Status": "Done", "Notes": "Inspector remarks here"}}],

    "OpCheck": [{"": {"Status": "Done", "Notes": "Inspector remarks here"}}]
}

(It's mostly abbreviated, because I wrote this based on the data provided as an image, and I did not want to transcribe everything. Hopefully, you get the idea.)

...

And, this is the exact same JSON (except text is now copied from the updated question), but prettified and validated, using more standard white space formatting:

{
    "Physical check": [{
        "Check existing printer": {
            "Status": "checked",
            "Notes": "Inspector remarks here"
        }
    }],

    "Printer visual check": [{
        "Check front of printer": {
            "Status": "checked",
            "Notes": "Inspector remarks here"
        },
        "Check ink levels": {
            "Status": "checked",
            "Notes": "Inspector remarks here"
        },
        "Check led lights": {
            "Status": "checked",
            "Notes": "Inspector remarks here"
        },
        "Check power cord": {
            "Status": "checked",
            "Notes": "Inspector remarks here"
        },
        "Check print quality": {
            "Status": "checked",
            "Notes": "Inspector remarks here"
        },
        "Check paper size": {
            "Status": "checked",
            "Notes": "Inspector remarks here"
        },
        "Check paper amount": {
            "Status": "checked",
            "Notes": "Inspector remarks here"
        }
    }],

    "Covers test": [{
        "Front cover test": {
            "Status": "checked",
            "Notes": "Inspector remarks here"
        }
    }],

    "Operative check": [{
        "": {
            "Status": "checked",
            "Notes": "Inspector remarks here"
        }
    }]
}

I know 3 JSON specifications : JSON-LD, HAL and JSON API. I prefer the second.

So I will write your json like this :

{
"buckets": [
    {
        "id": 1,
        "orange": 3,
        "apple": 4,
        "banana": 7
    },
    {
        "id": 2,
        "orange": 5,
        "apple": 6,
        "banana": 2
    },
    {
        "id": 3,
        "orange": 5,
        "apple": 11,
        "banana": 8
    }
]

}

@Andy's response is more like JSON API specification.