"I powered down the sub panel and put all the grounds on the left and the neutrals on the right. They are still bonded together as I only have three feeds form the main. " you are very likely to need to add a separate grounding bar to the panel, and possibly two (one on each side). the green bonding screw that ties the neutral bar to the box itslef must be removed. Some panels allow you to remove the bonding between the tqro strips so that one can be used for grounds, the other for neutral but this tends to make a real mess in the panel since every grounded circuit now needs to go separately to each bar. It is often worth the effort to add two grounding bars parallel to the existing neutral bars. This allows the neutral and ground for each circuit to be tied to the respective bars adjacent to the breaker feeding the hot for that circuit. It sounds like you need four #6 connections (though it might be possible to use a smaller ground line). The hots come from a breaker in the main, and the neutral and ground both come from the same point in the main but need to land on their separate bars in the sub. The reason ground and neutral are separated in sub panels is to prevent any current sharing between the ground connection back to the main and the neutral connection. Any voltage drop in the ground connection picks up the grounds in the sub-panel and the ground of every branch circuit is is supplying. Grounds are never supposed to carry current, except during a fault. You want the whole set of grounds to be as close to zero volts as possible.

You need to remove any ground to neutral bond in the generator itself. The generator will use the service grounding electrodes and conductors. Remember to bond the generator again if you use it for other purposes. In a main panel grounds and neutrals are bonded and may be mixed on the bars. They are separated in any other panel (sub-panels).

The majority of the switches and receptacles are not installed yet. Just enough for light and a few receptacles. Before jumping on the "electrician" here, I wonder whether the electrician did his or her version of a "rough-in", with the expectation of returning to install switches, receptacles and other fixtures before the circuits were put into service. If so, there may be other issues involved in moving from rough to final. What was the agreement as to the scope of work the electrician would perform? Who put in those few switches and receptacles that are already installed? Was the can you moved already energized (i.e., "hooked up" to a circuit with usable power)? If the electrician installed working switches, receptacles and lights with hots and neutrals connected but with grounds left unconnected and/or unbonded, then I'd definitely call him/her out on that. It's just plain wrong. If anything, most of the grounding work should be done at rough-in and the fixtures installed later. (And, naturally, you can't connect an EG to a fixture that's not there yet.) I plan to install the receptacles and switches myself so I know that will be done right. No offense intended here, but the nature of your original post makes me feel a little nervous about that statement. Are all the equipment grounds continuously bonded with only pigtails for fixtures left unconnected?

I'll be doing the work myself. It'll only be the cost of the bar and some time. I am capable of performing the work. Have done heavy ups before and have had inspectors approve them. I just don't know all the "rules" so to speak. Where I live there is no reqjirement to have electrical setup for range/dryer but I will be leavi ng the wires there. I am only going to be adding a single breaker to make a minor change. Just want to know the rules as I said. There will be no open spaces in the panel face. If there are I will install a blank plate.