Ok, I know similar posts have been made, and I've read dang near everyone of them, and still haven't found a solution to my problem.
I have a 2002 Edge Flex Fuel 3.0L auto. It has had a misfire since I bought it. I've replaced damn near everything, plugs, wires, injectors, coil, maf sensor, crank sensor, cam sensor, tps sensor, various gaskets, O2 sensors, brand new heads, and probably a few other things I'm forgetting about. I still have a misfire and recently it started idling very rough and smoothing out a little when driving, sometimes it will stutter and bog when going up a hill. If anyone has any fresh ideas, I'm open to them. I already took it to the dealership for some help, they did help at all, just took my money. Any help is greatly appreciated. Thanks.

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2002 Ranger Edge+ 3.0 Ext Cab 4dr Flex Fuel auto Throttle cable mod, air box mod with drop-in k&n filter, Screamin Demon coil with Live Wires, Buggman LEDs, stainless steel gauge cluster, tinted taillights, after market headlights, bull bar, step bars, and I even washed a few times.

Miles? Rent a compression tester and check on a cylinder that isnt missing and then on the missing cylinder (or do all of them)- is there a big difference?

Go to a muffler shop and have them backpressure test the cats. Rent a fuel system pressure tester and ensure you have solid fuel pressure (should be in the mid 60s). Get an old sparkplug, pull the missing cylinders plug wire, plug it into old sparkplug, and ground the plug against something (preferably not near the master cylinder or battery)- do you get a solid spark? Disconnect the MAF sensor and disconnect the battery for 10 minutes, reconnect the battery, leave the MAF disconnected, then start it- do symptoms persist?

Rather than looking at the big nightmare under the hood, try to isolate and shrink your problem: "I have a miss on cylinder 3. Cylinder 3 needs air, fuel, compression, and spark and at the right times for each." Then start nailing down whether each aspect is working as it should.

I should note that typically clogged cats or a weak fuel pump will cause problems over the entire engine (or bank of cylinders in the cats case)- I would be focusing on compression and spark for the missing cylinder. Also note that the longer you run with a miss, the more abuse your cat takes. Cats go through hell when dealing with raw fuel, and can easily become clogged presenting new problems (sounds similar to your new bogging issue)...

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2002 Ford Ranger XLT Supercab, 2.3L Duratec I4, 5-speed manual, 4.10 gears, ~100,000 miles
Power nothing with air conditioning; crank windows for life!
Throttle cable mod, retained accessory power mod, 2006 thermostat w/resistor mod
Headlight relay harness, Philips xtreme-vision bulbs
P235/75R15 Michelin LTX M/S2s

You replaced the injectors.....did you use ones for a flex fuel engine? Ask me how I know! lol

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'99 Ranger XLT 3.0 4x4 gold stepside
'99 Ranger XLT 4.0 2WD, RIP at 326,000 miles

Do the compression test I had a see what ur numbers are I had 70 psi in my #1 and a miss there turned out to be burnt and recessed valves and bad injectors