Hi Adam. To answer your question on running the game with USB Loaders, yes. Currently, all forms of USB Loaders (Dios Mios, Nintendon't, Wode, etc.) are allowed.
Now about emulating the memory card, I am unsure. Memory card emulation has been brought to my attention before, but the runner in particular chose not to submit their time. I don't know enough about it to tell you the advantages/disadvantages of using that feature. The most I can do right now is tell you that you are okay to use MCemu for the time being, and I will get back to you with a more solid answer.
However, my suggestion to you is to invest in an official memory card & game. Official memory cards are cheap and plentiful online, and sell for dollars via most online sites. Copies of the game are also pretty cheap, selling for around $20-40 online.
I know that the higher blocks, 1019 and up I think, on an emulated card are considered unstable by the devs so they could actually be slower. I might test that out.