Another congrats on setting up your new tank!
It seems that no matter how you do something, you always wonder if you could have done it better, chosen differently, etc. Like Clint says, you will settle in eventually, and so will your fish. Then you will be happy to have the extra space.
I'm not sure if carbon exactly kills plants directly.... to carbon or not to carbon has been such a debate that this topic has been locked on many planted tank forums. Everyone has a different opinion, and no-one seems to be able to agree. Some people use carbon and swear by it; others never use it and find alternate media to put in their filters.
One of the worst parts about carbon is that it cleans the water indiscriminately. There are three components to any filter: Mechanical, Biological, and Chemical. Mechanical filtration is the filter itself moving the water, keeping it from stagnating and moving it through the other media. Biological filtration is the filter floss, noodles, or bio balls which provide a surface for the growth of beneficial bacterias. These bacterias are essential in cleaning the water and keeping the tank in balance, moving the nitrogen cycle from one phase to another. Ammonia becomes nitrIte, which is in turn converted into the less harmful nitrAte by the bacteria. A filter can and does function with only these two components, but some people add the chemical as well. It clears the water of small particles, which is why you are supposed to take it out when medicating. The carbon will also remove any fertilizers you might add for the benefit of the plants. However, nothing cleans and clears the water better. If you have large or messy fish, carbon is beneficial and even necessary, but it loses its potency after two or three weeks and becomes another biological media. I personally find it helpful to run carbon for a week every month or two; it makes the water crystal clear. The rest of the time, I just pack the media chamber with other materials and let the bacteria do its work.
It can be scary to change something you have been doing for so long, but if you notice ill effects, you could always put it back. If you take the carbon out, I would recommend waiting until your tank has settled. For now it will help to take any particles of substrate, etc that have been disturbed in the move.
I am sorry to hear your Weather Loach is not well. If you have had him 10 years, he could be much older. Sounds like he is sitting at the maximum age for these guys. At least when he goes, you can feel good about the fact that he has lived a long, happy, and healthy life. It is an accomplishment to have kept him alive so long.
Enjoy your new tank:)
soul-hugger
Success is measured by the amount of obstacles you have overcome.