Yong Heng Simple to Hardcover rebuild

All the parts are retro-fittable. The parts in question are supposed to separate moisture between the low and high stage. I think that they do a reasonable job. IMO the basic version should be OK as long as you include a desiccant filter between the pump and bottle. Buying the model that you require would have been a better choice than buying a cheaper version and updating with spare parts. So the answer to your question is yes it's possible but is it necessary? Probably not.

If I was you, I wouldn't worry about the cyclone separator. It's beneficial but not essential. The filter that is in your link should be fine for filling or topping off a 4 litre bottle, just make sure that you use some sort of desiccant in it. I use one of those myself for topping off my 6.8 litre bottles. I have a larger gold filter filled with molecular sieve desiccant that I sometimes use, to fill a bottle from empty but I have found that it is not necessary for just topping off and is absolute over kill for filling guns because of the wasted air. If you live in an extremely high humidity area, it may be worthwhile to install the cyclone separator but otherwise just use the pump until you decide to get something better.

Starting with a fresh cotton filter element in that small black filter that came with the compressor, do you feel any wetness on the element after filling your gun ? If not, the filter should be able to absorb most of the water in the compressed air in one single fill. I would suggest keeping things simple by replacing the cotton filter element after every fill. Used filter elements can be reused after they dries out naturally.

Another way to get some water out of the air:

I had been using a Shoebox compressor that requires a seperate compressor as a first stage. My Pancake compressor runs about 1/20th of the time to keep the Shoebox supplied with first stage air and after awhile the tank on the first stage Pancake has to be drained of water condensate. It takes water out of the air going into the Shoebox and then the Shoebox further compresses the air and you get more water out, which the output filter should collect, if you have one that is. My Shoebox needs an overhaul after about 2 years of use and I decided to get a Yong Heng for less that $300 rather than overhaul my Shoebox and the Yong Heng is faster than the Shoebox.

Now, here is another notion to get water out:

Take your normal 150 psi compressor to feed the Yong Heng compressor through the intake port, set the regulator on the compressor to about 2-5 psi, do not set at 150 psi. The air will be compressed in the tank to 150 psi and water will be condensed into the tank which can be bled out of the tank and not go into the Yong Heng compressor, 2-5 psi air goes into the Yong Heng to be compressed to a max of 4500 psi. I only fill my tanks to 4000 psi to avoid the hard work of going from 4000 to 4500 psi, hard work means more HEAT and time. 

I think you are correct that adding the parts will change it to the Hardcover version and that it is a great idea. I have the YH with the water separator and it does separate a good amount of water from the compressed air. Yes, you can use a filter to do that but it will cost more as the filters will need to be replaced far more often than if you had the YH unit with the separator installed. I have the small YH filter and a gold filter with the three part media inside. I purge the YH unit every five or so minutes of run time and change the small YH filter out after every 20 minutes of runtime and it is damp. I set it aside and let it dry and use it on my next filter change. I have run my YH for a year and the large filter is still not in need of a change.