For GBA tile editors I tend to go with
Tiledggd can also be helpful but it does not edit thingshttps://github.com/puggsoy/tiledggd-pe-/releases
The GBA does make use of compression, and the Harvest Moon/Rune Factory line of things does some odd things here (in addition to the bugs and sloppy translations).
To that end you might have to work around compression.
If it comes to it then you can follow things back up the line to the ROM itselfhttps://www.romhacking.net/documents/361/
is for an older debugging emulator. Today we would probably suggest the debug version of http://problemkaputt.de/gba.htm
but the same logic/process applies.
There are tools that will either use emulator logs of compression calls to the BIOS, or fingerprints of the compression to search the ROM too.
I cover a few in http://www.romhacking.net/forum/index.php/topic,14708.0.html
and while I don't like them very much they do produce results at times.
When you come to recompress anything you edited you will probably want a tool called GBAcrusher. Being graphics you will almost certainly want the VRAM (video RAM) safe versions.http://members.iinet.net.au/~freeaxs/gbacomp/#BIOS%20Decompression%20Functions
has a copy, and some more on the compression used.http://problemkaputt.de/gbatek.htm#biosdecompressionfunctions
also has good stuff.
All that said the first line of attack for most people is to either grab the data from the VRAM when it is playing and search the game with a hex editor for that (then put the tile editor to that address), or to open something in a tile editor, set it to one of the GBA modes (while the GBA does have 8bpp, which not all tile editors will have hence the suggestions above, GBA 4bpp is more common on the GBA) and press down/page down a lot, you can try to narrow it further with what a VRAM/OAM viewer might tell you it uses.
You can grab palettes for the graphics* from the emulator itself (some tile viewers even support savestates, though they will usually only be for older versions of VBA), or you get to find them in similar ways to the other parts of graphics (dump from emulator and search ROM, tracing, or figuring out any formats for them like they are all here or before their associated graphics or something being the big three).
*console game graphics tend not to be straight images as much as paint by numbers, with the palette being the name for the selection of colours. Hence the term palette swap when the data remains the same but colours change.
You might also get lucky and find someone has documented it before you -- I am never sure why people want to mess around with the GBA editions of Harvest Moon (other than maybe the N64 stuff they are the last versions of the game I would probably suggest to someone I am trying to get in on the series or style of play) but you are far from the first to come here or other GBA ROM hacking places seeking to do something.