Never mind on the flash part. I got that figured out. All of the following
code was written with the ham 2.71 dev kit. This code also needs the MBV2
debugging libraries.

--------------Flash.s-------------------------
.GLOBL check_flashrom
.GLOBL switchbank0
.GLOBL switchbank1
.GLOBL writeflash
.GLOBL eraseflash

.ARM
@.SECTION .iwram
.ALIGN
.TEXT

@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
@@@@@@@@@@@@@@
@
@ Flash related functions.
@
@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
@@@@@@@@@@@@@@


@extern void check_flashrom(u16 *v1, u16 *v2);
check_flashrom:


STMFD sp!, {r2-r5}
ldr r5,=0xE005555
mov r2,#0xAA
strb r2,[r5] @ AA => 0800AAAA
mov r4,#0xE000000
ldr r3,=0xE002AAA
mov r2,#0x55
strb r2,[r3] @ 55 => 08005554
mov r2,#0x90
strb r2,[r5] @ 90 => 0800AAAA
ldrh r2,[r4] @ 08000000 => v1
strh r2,[r0]
ldrh r0,[r4,#0x1] @ 08000002 => v2
strh r0,[r1]
mov r0,#0xF0
strh r0,[r4] @ F0 => 08000000
LDMFD sp!, {r2-r5}
bx lr

@extern void switchbank0(void);
switchbank0:
STMFD sp!, {r2-r5}
ldr r5,=0xE005555
mov r2,#0xAA
strb r2,[r5] @ AA => 0800AAAA
mov r4,#0xE000000
ldr r3,=0xE002AAA
mov r2,#0x55
strb r2,[r3] @ 55 => 08005554
mov r2,#0xB0
strb r2,[r5] @ 90 => 0800AAAA
mov r2,#0x00
strb r2,[r4]
LDMFD sp!, {r2-r5}
bx lr

@extern void switchbank1(void);
switchbank1:
STMFD sp!, {r2-r5}
ldr r5,=0xE005555
mov r2,#0xAA
strb r2,[r5] @ AA => 0800AAAA
mov r4,#0xE000000
ldr r3,=0xE002AAA
mov r2,#0x55
strb r2,[r3] @ 55 => 08005554
mov r2,#0xB0
strb r2,[r5] @ 90 => 0800AAAA
mov r2,#0x01
strb r2,[r4]
LDMFD sp!, {r2-r5}
bx lr


@extern void writeflash(u16 address, u8 data);
writeflash:
STMFD sp!, {r2-r5}
ldr r5,=0xE005555
mov r2,#0xAA
strb r2,[r5] @ AA => 0800AAAA
mov r4,#0xE000000
add r0, r0, r4
ldr r3,=0xE002AAA
mov r2,#0x55
strb r2,[r3] @ 55 => 08005554
mov r2,#0xA0
strb r2,[r5] @ 90 => 0800AAAA
strb r1,[r0]
strb r1,[r0]
mov r2, #0xFF
strb r2,[r4]
LDMFD sp!, {r2-r5}
bx lr

@extern void eraseflash(void);
eraseflash:
STMFD sp!, {r0-r5}
ldr r3,=0xE005555
ldr r4,=0xE002AAA
ldr r5,=0xE000000
mov r2,#0xAA @ -> E005555
strb r2,[r3]
mov r2,#0x55 @ -> E002AAA
strb r2,[r4]
mov r2,#0x80 @ -> E005555
strb r2,[r3]
mov r2,#0xAA @ -> E005555
strb r2,[r3]
mov r2,#0x55 @ -> E002AAA
strb r2,[r4]
mov r2,#0x10 @ -> E005555
strb r2,[r3]
eraseloop:
ldrb r0,[r5]
ldrb r1,[r5]
cmp r0,r1
bne eraseloop
ldrb r0,[r5]
ldrb r1,[r5]
cmp r0,r1
bne eraseloop
LDMFD sp!, {r0-r5}
bx lr
--------------end of file----------------------

------------bios.s----------------------------
.GLOBL MidiKey2Freq
.GLOBL HardReset

.ARM
@.SECTION .iwram
.ALIGN
.TEXT

@extern u32 MidiKey2Freq(u32 wavedata, u8 cMK, u8 cFP);
MidiKey2Freq:

SWI 0x1F << 16
BX lr

@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
@@@@@@@@@@@@@
@ Undocumented function
@ Hard Reseet
@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
@@@@@@@@@@@@@

@extern void HardReset(void);
HardReset:

SWI 0x26 << 16
--------------end of file----------------------

-------------flash.c---------------------------
/*
* Created by using HAM 2.71
* Author: CaitSith2
*/

/***************************************************************************
******
* Includes

****************************************************************************
****/
#include "mygba.h"
#include "mbv2lib.c"

/***************************************************************************
*****
* Prototypes

****************************************************************************
***/

//bios.s prototypes
extern void HardReset(void);

//flash.s prototypes
extern void check_flashrom(u16 *v1, u16 *v2);
extern void switchbank0(void);
extern void switchbank1(void);
extern void writeflash(u16 address, u8 data);
extern void eraseflash(void);

//Internal prototypes
u8 readflash(u16 address);
int GetKey();


/***************************************************************************
******
* MULTIBOOT is interesting.
* If you write this on the top of your main file,
* the GBA ROM you build will automatically be capable of running both
* from FLA carts and, in addition directly over the MBV2 cable.
* If you do not need this, simply comment it out.

****************************************************************************
****/
MULTIBOOT

/***************************************************************************
******
* Program entry point

****************************************************************************
****/
int main(void)
{

unsigned char *a = ((unsigned char*)(0x08000000));

ham_Init();
ham_InitText(0);
ham_DrawText(2,10,"Waiting for Debug Console");
printf("Debug Console Found\n");
ham_DrawText(2,10," ");
ham_DrawText(2,11,"Do Not power off the GBA");
ham_DrawText(2,12,"Or unplug the MBV2 cable");


long i=0,j=0,k=0;
char filename[13];
char filespec[3] = { 'r', 'b', 0x00 };
int OptR=0;
int OptW=0;
int Size=0;

printf("Do What?\n");
printf("R - Read Save\n");
printf("W - Write Save\n");

i = GetKey();

if (i == 'R')
{
filespec[0] = 'w';
OptR=1;
}
if (i == 'W')
{
filespec[0] = 'r';
OptW=1;
}

if (OptR || OptW)
{
printf("What Size is the Flash?\n");
printf("1 - 64K\n");
printf("2 - 128K\n");
i = GetKey();

if (i == '2')
{
Size=1;
}
}

printf("Now Enter a Filename!\n");


while ((i=GetKey())!=0x0D)
{
filename[j] = i;
j++;
}

FILE *f;
f=fopen(filename,filespec);


if (OptW)
{

printf("Erasing Flash\n");
eraseflash();
// while((j=readflash(0))!=0xFF);
// while((j=readflash(0))!=0xFF);
// while((j=readflash(0))!=0xFF);
printf("Flash Erasing Complete\n");
for (k=0;k<=1;k++)
{
if (!Size)
{
k = 1;
}
for (i=0;i<=0xFFFF;i++)
{
if ((i % 0x0100) == 0)
{
ham_DrawText(1,10,"Flash Written to 0x%.5x",i+(k<<16));
}
j = dfgetc(f);
if(j!=0xFF)
{
writeflash(i,j);
}
}
if(Size)
{
switchbank1();
}
}
}

if (OptR)
{
if (Size)
{
switchbank0();
}
for (k=0;k<=1;k++)
{
if (!Size)
{
k=1;
}

for (i=0;i<=0xFFFF;i++)
{
if ((i % 0x0100) == 0)
{
ham_DrawText(1,10,"Flash Read from 0x%.5x",i+(k<<16));
}
j = readflash(i);
dfputc(j&0xFF,f);

}
if (Size)
{
switchbank1();
}
}
}
fclose(f);

printf("\n\nPress a key to continue\n");
GetKey();
while(1)
{
HardReset();
}
}

u8 readflash(u16 address)
{
unsigned char *a = ((unsigned char*)(0x0E000000 + address));
return *a;
}

int GetKey()
{
int i;
i = dgetch();
printf("%c",i);
return i;
}
--------------end of file----------------------

Now all I need, is the eeprom reading/writing code.