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Any ideas on better throttle response for what I have other than typical maintenance? (Plugs? Coil? Air Intake?)
I'm already looking at changing out the muffer for a single 3" in/dual 2.25" out piece for better breathing (currently has 2.25" turbo muffler that's "choking" the engine). So that will help regardless.
You will be much better off with a full 3" exhaust from y-pipe to tail pipe. Unless you want to line someone else's pockets for the dual 2.25" tailpipes they are a waste of money. Conanski and I have debated the long tube versus shorty headers before so that is up to you to decide what fits your budget. If you decide to stay with factory manifolds or shorty replacements you can use a Bassani y-pipe designed for the Bronco. It comes in two flavors, with cats or without. I used the without version so I could install my own personal preference ( Magnaflow spun series metallic core). From there I used a Magnflow 3" I/O center inlet/outlet muffler and finished it with a Dynomax/Walker 45683 tailpipe. I wanted that particular converter because it was one of the few with the proper ratings to handle a 5.8L engine and a truck with a GVW over 8500 lbs ( my truck is a F350). The muffler is a universal fit with a 24" body. The tail pipe is designed for a mid-90's Chevy truck. It is a free flowing mandrel bent 3" aluminized tailpipe. I found it at Summit Racing for ~$58 USD. I connected everything with stainless Dynomax/Walker band clamps (p/n#33272). They offer a more secure fit than standard clamps and offer the ability to remove them to adjust or replace your pipes/muffler/cat very easily.
I have had professionally installed exhausts on my vehicles for well over 25 years. This one was one of the best built and sounding exhausts I have ever had. And I did it myself in my home garage without a welder. I spent around $600 including two new factory style exhaust manifolds. If your manifolds are good you should be able to duplicate my setup for around ~$400 USD.
I agree with Conanski, even with the exhaust upgrade you will not see a huge improvement without changing the heads and cam. E7 heads will only flow so much. GT40/GT40P or aftermarket heads will be needed to maximize the flow potential of a GT40 intake investment.
It already has the 2.25" duals from the previous owner, so money saved there. I intend to keep the factory manifolds provided they are not leaking (have an exhaust leak near the engine).
For my budget, the muffler swap and splicing in a pipe for proper fit is all I can do. However, I do like your 3" single idea for down the road.