1987 MR2 AW11. Red top engine, blue top ECU with a flat spot at 5,000 rpm.

Hello,
I hate to ask a question which has the obvious answer "just google it". But here it is anyway. 
Facts first:
My car was Australian delivered and converted to a small port engine after a lack of oil mechanical failure.
It has the original TVIS injectors that have been flow tested and verified for CC's and spray pattern. TVIS dizzy and coil assembly, TVIS ECU. Most of the TVIS VAC solenoids and plumbing are also present and presumably blocked. The knock sensor and lambda are both unused. It has an A/F flap style sensor. The original intake route through the boot is still used.
Subjectives:
From 2000 to 4750 rpm it has plenty of torque. It has reasonable throttle response in 5th from 2500 rpm up on a flat road.
At around 5000 rpm it gets into a big flat spot. Im reluctant to leave it at these revs for any length of time as the mapping just feels wrong. From 5500 to ????? rpm it goes on cam as expected. I haven't done this a lot due to the previous issue noted. Changing up at these revs gives a single exhaust pop on over run.
Questions:
Is there a respected "red port engine/tvis ecu" hybrid guide on the web that explains what is required to make this conversion work?
What octane fuel are people using with this combination? (Im using 98 until Im told otherwise.) 
What static advance are people using with this combination?
Im guessing the flat spot is related to the tvis change point. From what I've read it momentarily increases spark advance and opens a vac actuator at the change-over revs.
 
Im in Melbourne and the car and its history are new to me.
Regards,
SteveB
 
 
 

Thanks feral4mr2.
1. The induction side is small port up to the throttle, then it is the original bigport AFM, resonant box and sensors.
2. Previous owners choice on the O2.
 
Ive now tried 98/95/92 octanes and it seems to run pretty well on the two lower octanes. The issue is still there, but it seems ok for the short term.
SB