This site is not for solicitation of services or 'purchasing' development. Please do not post requesting side mods/plugins and so on. Your thread will be removed, and you will receive a warning.
It helps to enchant those diamond hammers that you're creating. If they get Efficiency and Unbreaking, the hammers will last a while and pokeballs can be made easily and quickly. I've made an Efficiency V and Unbreaking III diamond hammer and it's so fast, pokeballs will be really quick to make. Early on without diamond hammers or enchantments, it is tedious, but through your time spent playing, it gets easier when you begin to unlock these.
Again, I haven't read your entire paragraph, so I don't know if you've tried this, but in the Pixelmon configuration files, you can edit a configuration to allow finished lids and bases to be instantly replaced on anvils.
It's good that you're still required to scavenge for resources to make pokeballs and once you advance in the world, these things are less troublesome. So when you travel the map to look for new pixelmon, take the time to mine around and look for exposed coal, iron ore and bauxite ore.