Just an update.
Im close to solving menu problem. Looks like the chipset modes were never being set right from the starts.
Hoping to have it fixed in the next few mins,
.
Did'nt work,

.
I know why its not working, but just trying to workout a way around it.
Basically, we have AGA as option 4 in the menu.
Now the emu take 4 as CSMASK_AGA. Which is what you would think is selecting AGA.
Well its not, as for a proper AGA state, you need to have CAMASK_AGA, CSMASK_AGNUS and CSMASK_DENISE all set.
Now the problem is, the true value for option is 7. This puts the menu to an option that doesnt exist (i.e. null).
Settings;
0 //OCS,
1 //ECS_AGNUS,
2 //ECS_DENISE,
3 & 4 //ECS_DENISE | ECS_AGNUS (Full ECS),
5, 6 & 7 //AGA | ECS_DENISE | ECS_AGNUS (Full AGA).
As you can see, 5, 6 and 7 need to be set for proper AGA.
Im proberly missing something simple, will keep playing with it.
This problem has also opened my eyes to HDD options, maybe this could be answer to HDD not booting issue.