RxTools refused to boot for several attempts before it would load. and when it did load, it refused to load up any of the GBA or DSiWare when I tried using it. And exactly two reboots later, rxtools refused to launch at all, even when reinstalling its purported DS Profile exploit installer. Yet nobody here would help me on the matter, and nobody had an answer for me then, either. I only even started considering CFW so I could finally launch and run my Ambassador GBA ware, my legit DSiWare, and in part because of seeing some already porting some of the better GBA games in .cia format, that I recognize I can't currently launch at all on Gateway. But Gateway does let me run out-of-region games, and has a thorough and powerful cheat support. So I would need to retain that functionality. As good as CIAngel is, it doesn't even attempt to load half the games available on the real eShop, and I've been unsuccessful in finding a download for this supposed "freeshop" anywhere, even though I've even encountered a few streetpass Mii's that have been using it.
How long ago where you trying to use RxTools? Its been depreciated (and quite frankly broken) for a few months now, and gba/dsi support for the n3DS on RxTools has not worked since early October of last year. If I remember correctly, that was about the time it broke AGB/TWL support for all consoles.
As for a download for freeShop, you must not of looked very hard.
http://lmgtfy.com/?q=freeshop
Admittedly, google search now adapts based on browsing/search history, but the first link returned SHOULD be either the thread here, a thread on reddit, or the github page for the software itself.
PLailect's guide would require me to kill the DS profile exploit that I've been using since the first day I got the GW. Its instructions have me update to 9.2, then downgrade to 2.1, before I even get to where I would install its so-called "glorious master race" exploit that it's supposed to be for. So an upgrade that automatically kills the 'sploit that has kept me safe in emuNAND, and then a downgrade to a firmware that is older than what the system first shipped with, and you don't see a problem with that? It's well known on the PS3 side of things that if you didn't keep on 3.55 OFW, you were boned for anything CFW related, and that you couldn't even downgrade at all without some extra hardware nobody wants to make anymore. I might have some soldering skills, but I'm nowhere near the level of soldering in a hard mod set of parts to restore this system from a brick.
You just said yourself that downgrading a console is not exactly a new concept in CFW. The difference here is that you don't need hardware at ALL to downgrade. Its entirely software based.
Since you seem to be adverse to actually reading the entirety of the guide and are getting hung up on how the steps seem counter-intuitive to you, I will try and explain what happens, how it happens and WHY it HAS to happen.
In order to install A9LH at all, you need a dump of a console specific encryption key register. This is the OTP.bin file that you keep seeing/reading about. It HAS to come from your console as every console has a different set of keys. Starting in 3.x, the system locks/encrypts this file before the arm9 processor is initialized, and since the earliest we can obtain code execution IS the arm9loader, we cannot under any circumstances unlock it. However in 2.x, the file was not locked until after the firmware was loaded. Meaning we could dump and view/use the file if we could just get arm9 code execution. We have to downgrade specifically to 2.1 because this is the only firmware with a reliable arm9 exploit.
Now, the guide has you back up your emunand, sysnand and SD card (complete with any and all games, NNID info, saves, EVERYTHING) before even starting any downgrade steps. You will (over the course of several steps that are ALL necessary) downgrade your emunand to 2.1 using a downgrade that triple checks the files being installed, the files already installed, and the files AFTER being installed to ensure that everything installed properly. If at any time it errors out, all you have to do is load up a program that the guide has you put on the sd card called decrypt9 and restore one of the emunand backups it had you make at the start.
Once on 2.1, you will run a program that completes several steps at once, independently checking EACH STEP for verification before it moves on. It once again checks the state of the 2.1 emunand to make sure its not completely borked. It fixes some encryption/cleanup issues caused by downgrading. Then it copies the emunand back over to the sysnand. At this point you have a 2.1 sysnand that can be used to dump the otp.bin. The guide will have you boot the sysnand and use browserhax to load an installer for a9lh that dumps the otp.bin and installs a9lh.
Finally you flash your original backed up emunand (with all the games, saves and other goodies) to your sysnand using a new program called Hourglass9 that does not overwrite the a9lh files. You then restore your sd card backup and carry on with Luma3DS as a cfw, with a 100% boot rate (even better than gateways ever was).
EDIT:
Please do not use my "synopsis" as a template for "things you can skip". You need to read and follow the ENTIRE guide (I know, I know, reading is for plebs and sucks horrid things. Deal with it.).