I can't really help you, but to avoid those kinds of problems. I swapped on the 4.0 head and went with the offy intake and holley 4 barrel setup. The holley TA 4 barrels are built for off road and will take some extreme angles. Also there's no computer or sensors to worry about. I've found this setup to be reliable and capable, easy to maintain. I known it's too late to go back. Some one will be a long to give you some advice. Good luck with it.
1987 wrangler, 258 I-6, 5-speed.
2007 liberty sport 4X4, automatic
2009 ford ranger 4x4 FX4 OFF/ROAD, 5-speed