My opinions only.
Wiring on Ford EFi's for 88s is sub par, so updating to another MAF EECIV might require as much work as a MegaSquirt. I'd keep your stock emissions stuff intact, and add a MegaSquirt. Keep your stock EECIV computer, and allow it to run the EGR and AIR and just use the MegaSquirt for key fuel, ignition and MAF sensor system changes. A GM MAP sensor and MAF sensor conversion are what the plug and play uses, so you can split the stock computer and use the PNP as an auxiliary fuel and ignition and MAF system.
Ford for a few years used a break out box attachment in the days before the 1991 truck's live data streaming. Crane Interceptor, Extreme Edge, Actron Break-out Box. They allow you to double tie the 60 pin connector. That allows you to keep the stock wiring pinouts, but you can live data feed via TunerStudio from MS PNP. In a similar way, Quarterhorse uses a J3 port, a very good system, but for 200 bucks you can multiplex your EECIV pinouts to the critical Malfunction indicator light parts, and have the MegaSquirt take over fuel delivery, ignition and boost.
I'm giving you advice, not telling you what thou shalt do. If you truck was a 95 or 96, I'd be suggesting the EECIV or V.
How it works for emissions and simplicity varies a lot. The blended approach then allows you to fix the two biggest problems with an early EECIV...they don't like any changes to the speed Density program, they have to many problems updating to MAF because if the transfer function, and the stock injection and ignition system isn't mapped for updates.
Your going to be using much better injectors, and the air pump can be used as
i lag. The
's can stay. The high low fuel pump system can stay stock with its normal pressures boosted, EGR is a proven closed loop knock reducer, so stock wiring can feed through the stock TPS and MAP signals. MegaSquirt uses a recommended sensor type and if turbo, MAF is better.
Gotta say, any changes from the stock wiring or fuel delivery on any 1989 US EECIV vehicle is a guaranteed Major Project Rewire and Pumps and Hose rework. I'd buy the two pumps, and keep all the crash switch and pickups and returns stock, but redo the lines with better quality AN fittings. You want to keep the power steering, air con, the KOEO/KOER fault coding, and have no problems with any of the annual inspection or licencing.
With the money saved on not doing a full rewire, spend big on a much better cam reprofile by Schneider and some forged pistons and better conrods. And don't be afraid to get the head ported and the valve train updated to suit a 525 thou cam lift.