You have way WAY too much airflow in that TB there. A full race strip only 2.3 does whatever it can to keep up with 600cfm. The intake you have won't flow enough to keep up with TB either. Betting any software you have for it will be for V-8 as well and way too much of everything there. The engine in any form other than supercharged cannot use 1000 cfm or even close.

1000 cfm on a four is like 2600 cfm on a big V-8, or a pro stock engine at 10,000 rpm and no power below 6000 rpm. Low end power, you gotta be kidding. Bigger valves kill low end power as well, I'd be revisiting whoever is advising you.

Maybe you can figure out a way to use just two barrels only of TB............ .........and YES long tube header a must, not having it there will only make your problems worse and a bad combination already. The norm is a 390 cfm 4 bbl. on a hot street 2.3, you're off the map there.

Just because one has injection does not mean instantly it will tune out to work. No way not nearly. The software will be written with parameters that fit the intended use and 1000 cfm TB is a V-8 part intended for V-8 flow. Ford 2.0s and 2.3s are some of the b-tchiest engines made on earth when it comes to being overfed with whatever you use, carb or FI, they instantly spit out their guts and zero power with too much air capacity. Only way you can overcome that is by supercharging, turbo or other.