Reads like you are running too lean.
Stumble, hesitation and back fire are all signs of Lean.
Computer tries to keep air:fuel at 14:1, that's 14 pounds of air to 1 pound of gasoline
MAF(mass air flow) sensor is the start of that, it measures how many pounds of air are coming in.
Computer then uses that measurement to add the needed pounds of fuel.
I notice you mentioned air box sealed tight, I assume you mean the air tube from MAF to intake, so you know how important it is that ALL the air coming into the engine needs to pass thru the MAF or computers 14:1 calculations will be off, it will be lean.
I would unplug the MAF sensor and start the engine, CEL should come on right away, but engine should still start and run.
O2 sensors have the final say as far as computer is concerned.
But O2 sensors only work when they are above 650degF, so on cold engine there is no O2 feedback until engine warms up a bit, usually about 5minutes
O2 sensor can only see Oxygen, not fuel, so Lean mean too much oxygen, Rick means too little oxygen, it has nothing to do with fuel specifically.
Since your '99 has OBD II you can watch live data on your smart phone if you get a $25-$40 Bluetooth OBD II reader, this works on any OBD II vehicle, so any vehicle since about 1995, not a bad investment, and of course it is wireless.
You can then watch the fuel trims while driving, at idle +5 to +10 is normal
While driving -5 to +5 will be seen if everything is working well.
'99 computer would expect 70psi fuel pressure, if fuel pump was starting to get warn it might be 40-50psi, so computer would be injecting less fuel than it thinks, so Lean
TPS(throttle position sensor), this is like a light dimmer or volume control, a variable resistor.
It can get a dead spot.
Computer sends it 5volts
If throttle is closed TPS sends back .9volts
If throttle is wide open TPS sends back 4.8volts
In between closed and wide open the voltage varies the way you would expect, it goes up from .9volts.
If there is a worn/dead spot, voltage may drop suddenly causing computer to reduce fuel thinking you have closed the throttle when in fact throttle is still open, so.......Lean condition.