You have a few options. None of which will be free unfortunately unless you are able to fool Nintendo into fixing it if it's under warranty.
1.You should first try and end the 3DS to Nintendo for repair if it's still under warranty. Of coarse you should not mention that you used a flashcart on it. Just tell them the power went off during a system update or something. I've heard Nintendo has no way of accessing the contents of a bricked console. They'll probably just replace the whole console. This likely means they'll send you back a 3DS with the latest firmware, so say goodby to running 3DS mode flashcarts on it.
1.5. If step one was successful and you got a working console back from Nintendo. It will have latest firmware. If you still want to run a 3DS flashcart on it, you can sell it on eBay or similar site for a much higher price then you could with a bricked/non working console. Thus replacing it with a new 3DS that does have 4.5 or older firmware won't cost near as much and might be cheaper then paying $100 to Gateway to fix it. If however they refuse to fix it for any reason, then you must proceed with the last two options.
2. Sell bricked console on eBay for parts. Even bricked 3DS should sell for a somewhat decent price as it can be used for parts. Then use that to discount the cost of buying a new console to replace it.
3. Buy a Gateway. Once you receive it, send the 3DS to them for repair along with the gateway red card and any other things from that they require as per their instructions. Be sure to wipe your SD card (not the MicroSd card, the one in the SD slot for the 3DS) and put the gateway launcher on it. Don't be dumb and leave the one from your clone on it. Then they should fix it for you. You only really have to pay for shipping it to them.
However if they find out that the clone was the cause of the brick they may still fix it, but will charge you $100 or something to get it back. Which may be a cheaper solution for you as you may end up spending more replacing the console anyways.