Thanks Thorsten I will give that a try. 
Just to make sure that the MIOS was infact installed correctly, i reuploaded the mios_v1_9c_pic18f452.hex file. Firstly it would say "Starting upload of mios_v1_9c_pic18f452.hex
Hex file contains code in MIOS range, forcing reboot!" But then it would not progress from there. So i put it on manual mode, which then said:
Sending block 00000400-000004FF
Sending block 00000500-000005FF
Sending block 00000600-000006FF
Sending block 00000700-000007FF
Sending block 00000800-000008FF
Sending block 00000900-000009FF
Sending block 00000A00-00000AFF
Sending block 00000B00-00000BFF
Sending block 00000C00-00000CFF
Sending block 00000D00-00000DFF
Sending block 00000E00-00000EFF
Sending block 00000F00-00000FFF
Sending block 00001000-000010FF
Sending block 00001100-000011FF
Sending block 00001200-000012FF
Sending block 00001300-000013FF
Sending block 00001400-000014FF
Sending block 00001500-000015FF
Sending block 00001600-000016FF
Sending block 00001700-000017FF
Sending block 00001800-000018FF
Sending block 00001900-000019FF
Sending block 00001A00-00001AFF
Sending block 00001B00-00001BFF
Sending block 00001C00-00001CFF
Sending block 00001D00-00001DFF
Sending block 00001E00-00001EFF
Sending block 00001F00-00001FFF
Sending block 00002000-000020FF
Sending block 00002100-000021FF
Sending block 00002200-000022FF
Sending block 00002300-000023FF
Sending block 00002400-000024FF
Sending block 00002500-000025FF
Sending block 00002600-000026FF
Sending block 00002700-000027FF
Sending block 00002800-000028FF
Sending block 00002900-000029FF
Sending block 00002A00-00002AFF
Sending block 00002B00-00002BFF
Sending block 00002C00-00002CFF
Sending block 00002D00-00002DFF
Sending block 00002E00-00002EFF
Sending block 00002F00-00002FFF
Sending block 00003000-000030FF
Sending block 00003100-000031FF
Sending block 00003200-000032FF
Sending block 00003300-000033FF
Sending block 00007C00-00007CFF
Sending block 00007D00-00007DFF
Sending block 00007E00-00007EFF
Sending block 00007F00-00007FFF
Upload process complete
So i thought all was good. However when i reboot the core, it sends alot of sysex messages followed soon after by the random midi messages (as the unused pins are not clamped to ground)
This is what the midi in box says:
Sysex message: F0 00 00 7E 40 00 0E 0B 01 F7
00000000018160 ms | Sysex message: F0 00 00 7E 40 00 0E 0B 01 F7
00000000018164 ms | Sysex message: F0 00 00 7E 40 00 01 F7
00000000018166 ms | Sysex message: F0 00 00 7E 40 00 0E 0B 01 F7
00000000018170 ms | Sysex message: F0 00 00 7E 40 00 01 F7
00000000018175 ms | Sysex message: F0 00 00 7E 40 00 01 F7
00000000018187 ms | Sysex message: F0 00 00 7E 40 00 01 F7
00000000018190 ms | Sysex message: F0 00 00 7E 40 00 0E 0B 01 F7
00000000018193 ms | Sysex message: F0 00 00 7E 40 00 01 F7
00000000018195 ms | Sysex message: F0 00 00 7E 40 00 0E 0B 01 F7
00000000018199 ms | Sysex message: F0 00 00 7E 40 00 01 F7
00000000018201 ms | Sysex message: F0 00 00 7E 40 00 0E 0B 01 F7
00000000018205 ms | Sysex message: F0 00 00 7E 40 00 01 F7
00000000018207 ms | Sysex message: F0 00 00 7E 40 00 0E 0B 01 F7
00000000018210 ms | Sysex message: F0 00 00 7E 40 00 01 F7
00000000018213 ms | Sysex message: F0 00 00 7E 40 00 0E 0B 01 F7
repeat for a while then:
00000000026219 ms | [D0 00 00] Channel 1: Channel Pressure value: 0
00000000026220 ms | [D0 00 00] Channel 1: Channel Pressure value: 0
00000000026220 ms | [D0 7E 00] Channel 1: Channel Pressure value: 126
00000000026220 ms | [D0 40 00] Channel 1: Channel Pressure value: 64
00000000026221 ms | [D0 00 00] Channel 1: Channel Pressure value: 0
00000000026221 ms | [D0 01 00] Channel 1: Channel Pressure value: 1
00000000027470 ms | [82 00 00] Channel 3: Note Off C-1 velocity: 0
00000000027471 ms | [82 7E 40] Channel 3: Note Off F#9 velocity: 64
00000000027471 ms | [82 00 01] Channel 3: Note Off C-1 velocity: 1
00000000028719 ms | [F6] Tune Request
00000000030470 ms | [C0 00 00] Channel 1: Program Change no: 0
00000000030470 ms | [C0 00 00] Channel 1: Program Change no: 0
00000000030470 ms | [C0 7E 00] Channel 1: Program Change no: 126
00000000030470 ms | [C0 40 00] Channel 1: Program Change no: 64
00000000030471 ms | [C0 00 00] Channel 1: Program Change no: 0
00000000030471 ms | [C0 0E 00] Channel 1: Program Change no: 14
00000000030471 ms | [C0 0B 00] Channel 1: Program Change no: 11
00000000030472 ms | [C0 01 00] Channel 1: Program Change no: 1
00000000035219 ms | [90 00 00] Channel 1: Note On C-1 velocity: 0
00000000035219 ms | [90 7E 40] Channel 1: Note On F#9 velocity: 64
00000000035220 ms | [90 00 0E] Channel 1: Note On C-1 velocity: 14
00000000035221 ms | [90 0B 01] Channel 1: Note On B-1 velocity: 1
I hope i haven’t blown the pic up 
If I move sliders or pots on my midi keyboard (through which the core is routed) it comes up correctly in the midi in section.
Does this all look ok?
Thanks again.