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At least part of your problem is your alternator/battery combination has problems which might? at least partially explain your "miss" which could actually be the alternator cycling on/off.
First DIY check. Pop the hood and the silly plastic engine cover; grab a good flashlight; in Park & with brake on crank the engine up and let it idle; exit the vehicle; stand on the side just forward of the left front wheel and shine the flashlight down the slope of the serpentine belt to the serpentine belt idler. Is the idler nearly rock steady or is it doing a rock and roll dance? If the latter then your alternator decoupler pulley is shot. Replace ASAP before it takes out your serp belt/serp belt idler and possible causes engine to jump time. With luck you can source a lifetime warranty alternator with decoupler from line AutoZone.
If that DIY doesn't work go to any decent mechanic shop and have them load test the battery and check the alternator output.
X2 on the GDE tune but if you are running the 1st gen fuel filter head (driver's side electric plug is NOT bright blue) get the 2n gen one, see Sir Sam's NOOB guide bleeding video for PN. It's and easy DIY - undo fuel hose clamps; push not pull the hoses off the hose barbs; unplug the 2 top electrical plugs; undo 2 IIRC bolts holding unit to mounting plate; lift out carefully (there is enough wire) and unplug WIF sensor wire on bottom; if your current fuel filter is new save it for future use/same for old WIF sensor. Install of the new filter unit is the reverse PLUS wire in new fuel heater pigtail - undo battery; cut old wiring; insert new wires thru front of new plug and secure with blue retainer; connect new wires to old ones based on best fit match by size (colors won't match) using solder (not acid core)+heat shrink tubing or marine grade butt connectors with built in heat shrink tubing; plug in; reattach battery.
Check trusted mechanics posts for ones in your area.
_________________ Sold to LOST member my 05 Ltd, GDE Stg II turbo + TCM tune, SunCoast TC w. Transgo kit, Steiger window regulators, Samcos, Fumoto valve, 2nd gen filter head with Lub. Spec. bleeder, Hayden clutch & 11 blade fan, inverted spare, P-1 battery, BF Goodrich Long Trail TAs, Etecno1 glow plugs, timing belt at 50K miles/8 yrs
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