[Affe]

Well if you're not willing to lose your main, don't bot on it.
I did the exact same thing where I made a second account just to mine/harvest nodes. I only did this because too many people knew my main account and would smell something fishy.
I'm pretty sure the only way to get on SE's radar from mining is to mine with an AFK tag, teleport mine or running 24/7 and people report you. The more questionable things you do will put you closer to being banned. If you mine with an AFK tag while teleporting 24/7, you'll most likely get banned pretty fast.
For the gil and shards, there's not many ways to transfer. If you're doing it for RMT, you can trade with your bot account to the buyer. If you're looking to improve your personal fortunes, you can just mail it. I mailed from my bot account to my main for a month without any problems. If you're paranoid, you can put an item up on market for x amount of gil and have your bot buy it out. You keep the item in your possession but you get the money to your main.

Thank you very much! Your post helped me a lot :). And it is for personal selfish ingame gain :p.