I'm running a 347 Stroker in my 1987 Fox. It ran ok with the GT40 Heads and 30lbs injectors and stock throttle body and speed density.
You got lucky that this ran.
SD works by taking readings of absolute manifold pressure. From there, it is combined with a predetermined fuel table and sends an injector pulse width signal that is designed specifically for a 19 lb injector.
If it ran at all, it means that your combination of intake and injector size got you [close] enough for the engine to run. Who knows what your air/fuel mixture is across the useable RPM range but I can't imagine that it's good.
The first thing that you are going to need is a way to measure your air/fuel ratio. Once you are able to do that, you can make the determination about how far your current fuel system is from supplying the engine combo.
Your option from that point on are simple:
1. Bring your air/fuel ratio in-line by mechanical means
2. Bring your air/fuel ratio in-line by means of digital tuning
When you had the smaller throttle body installed, it caused manifold vacuum. No idea how much or at what RPM but it was enough to allow the car to run in combination with the other parts that you happen to have installed. Swapping out that throttle body dramatically reduced the vacuum in that manifold. It likely reduced it enough to make any signal from the MAP sensor, unuseable. It has certainly moved the bar enough to make it unable to support combustion in combination with your other parts.
There are several things that I could think of that you could try to bring it back in-line but they are all useless without the ability to read your air/fuel ratio.