Incorrect Speed and weird running

I'm having some trouble reading the speed and I'm wondering if anyone here has a setup similar to mine. I can get some screenshots later tonight but I may forget once I get home so I'm writing something now.

I have an LE5 in a Miata that became an Exocet (kit car). I got an electric VSS which I have wired into the E67. I am not using the Miata gauge cluster, but a Raspberry Pi with a screen. In HP Tuners if I set the gear ratio to the correct ratio (4.3 for now) and if i could set the VSS pulses/rev to ~9.3 I would get the correct trans output shaft rpm reading. However, the computer gets pretty angry when I do this. 1st, 3rd, and 5th gear act like I am in neutral (revs limited, high spark advance, etc.). But the speed is correct (also putting the wheel revs/mile at the correct number). So to fix this I can adjust the numbers, such as VSS ppr to a large number like 30. I think what happens is the ECM acts like it's in first (regardless of the actual gear) and allows some fudging of revs/speed. The speed output of the ECM is about 1/10 of actual (at 50mph it reads about 5). I have to keep this speed low enough otherwise it will go into "neutral" mode in fifth gear.

I'm guessing that when the speed is right the ratios are close enough in second and fourth that it works (fourth is almost always 1:1 so it makes sense), but it's unusable in 1st 3rd and 5th. Has anyone dealt with this here? Is there an easy fix? Otherwise I'll just have to leave it be and adjust the speed in my RPi dash.