you can try 64-bit version of WinUAE by renaming it to "winuae.exe" but I would generally recommend the 32-bit version.
Regarding the memory size, OS4.1FE in FlowerPot shows "126MB FAST RAM" by default. As soon as you install "Update 1" for OS4 and restart Flower Pot completely (reboot is not enough), it shows "646MB FAST RAM".
If it doesn't, it means you haven't installed the "Update 1" correctly or at all.
Here's my recommendation:
1. Rename your already installed "FlowerPot" folder to eg. "FlowerPot BAK" for instance. You can find it in C:\Program Files (x86) folder.
2. Go to Windows settings > Apps and uninstall Flower Pot (don't worry, your BAK folder will survive).
3. Now install FlowerPot.exe again. Let me know if you need the installer again and I will re-activate your download link. Just let me know the email you used to purchase it.
4. Now temporarily forget everything you think you know about OS4 and its installation ;) And just follow the Flower Pot guide EXACTLY. Nothing more, nothing less. Check the video mentioned above if you're not sure.
5. Now you should be looking at fully colorful OS4 desktop with 126MB RAM.
6. In Windows, unpack your "AmigaOS4.1FinalEditionUpdate1.lha" using WinRAR, for instance.
7. In OS4, locate the unpacked folder and just double-click the Installation icon.
8. When it's finished, quit Flower Pot and start it again. Now the OS4 desktop should show 646MB FAST RAM.
9. OPTIONAL: In Windows, replace FlowerPot\WinUAE\winuae.exe file with newer file from www.winuae.net (ZIP archive, 32-bit).
10. OPTIONAL: Before you start modifying your OS4, in Windows I recommend to backup FlowerPot\FlowerPot.hdf file. It now includes a working OS4.1FE+Update1 so you can start over from there if anything goes wrong in future.
Hope it helps!