congrats on your purchase. i too drive an e99 zf6 quad cab drw 4x4. i'm sure you have checked your alt to make sure it's working properly. if that alternator isn't keeping up or borderline then that will effect the injectors. your clutch issue......the e99's used a diff throw out arm then late 99's, because ford quickly realized the e99 wasn't strong enough. they crack then flex and you wind up having to push the pedal all the way to the floor. that is one tell tell sign you might have a cracked throw out arm. when changing trans fluid, some pump new atf in through fill port on the side of the trans. i removed the shifter last time and poured it in there. i say this as that really free'd up the stiff detent! now after a few thousand miles the stiffer detent is back, as it had been since mile one on the truck. tells me there isn't enough lube getting to that socket imo. imo the e99 has the best turbo for bottom end and mid with a little top end. once turned up say 80 hp tow via a tuner, it doesnt breathe the best at 75 mph (3.73 gears) pulling a load. i say that based on egt's alone, hauling a 34' fifthwheel camper, only weighing 11k lbs but 12'6" tall. kc turbo has a very nice drop in turbo for the stock up pipes. if you make the change then go with kc's 363/68 .91 as that will give you the top end with out deducting too much off of bottom end. it will perform well with stock inj's as well. if you decide to swap the inj's some day then i personally would go with AD ( late 99's) with 30% tips and some " custom " tunes in a hydra tuner. unless you need to double the rwhp then 205/30's are max on that kc drop in turbo. if add a hydra tuner, make sure and get the 90* usb head so that you can leave the cord plugged in and remote that port by the obd2 connector..... in case you want to up load someone elses tunes. the manuals are tougher to write tunes for but the e99 ecu is even harder to get decent tunes for. so far i have tried php, jelibuilt and 1023. in my truck for my application, 1023 tunes were unusable. php are the best for power int he wind but jelibuilts have the best pedal (tps) input while towing. i have been wanting to try allens tunes from AA tuning as i believe he took over for bill at php?? not sure of that though. in stock form the inj's cannot feed enough to overspin the stock turbo. un plug the waste gate controller and plug it onto the boost tube boot clamp bolt. i first tried the ww2 comp wheel in the stock turbo just to see. it did quiet it down but that was about it. while i had the turbo off i tightened up the wg controller 1 full turn, just so be sure it didn't float for any reason.
towing that fifthwheel listed above i ran a dp tuner, ww2 comp wheel with an afe stage II intake and full exh. if i were to do the exh over again i would use the stock dp and pull the cork out of the lower. larger exh does make a diff but not sure how much as i never tried. 28 psi was all she had in a 80 tow tune, in the wind, pulling grade, would see 1300* often and that just wasn't quite enough power to maintain ground speed. so i decided to swap out to hybrid 205/30 inj's, adrenaline hpop, t4 ss up pipe conversion kit, borg warner sxe 363 turbo, high v high freq idm, riff raff fuel cross over with fpr kit as well as high flow fuel fittings. 35 psi no problem now and egt's only hit a max of 1200*. i also discovered that the factory leaf springs didn't like the increased tq so ouo traction bars. i now have 139k miles on the truck and still love the truck. i had a low pitched chirping noise that sounded like a pulley starting to seize. so i replaced the tensioner and idler pulley's. didn't fix the issue and it turned out to be the power steering pump dragging a bit. sucked all the atf out of it ( yes it's atf not regular power steering fluid) refilled then ran and repeated until the fluid was clean. that stopped the sqeaking and made a noticable diff in idle as well as power steering. never knew a little drag on the belt would effect these that way. at that same time i began noticing that the coolant temps were 10 to 15* higher then normal under a load. the water pump wasn't leaking nor was i loosing fluid but had ran into an issue with a semi plugged radiator on my '92 7.3 idi. the thermostat necks are known for rusting out on these sd's so do yourself a favor and buy the aluminum version riff raff sells. i went ahead and replaced the cooling fan clutch, water pump and radiator while i was at it. the water pump bearing was on the verge of going out and the shaft was starting to deflect to the point where the impellor blades were just starting to make contact with the case. had a clean cresan moon shape on the block but just surface scuff at that point. so between that drag, the ps pump, it idles better with improved steering. another important note is that your abs module has been discontinued. remember that if you go to bleed the brakes! if it comes time for new wheel bearings the e99 are diff then late 99 and e99 is no longer available from ford. you will have to swap out to late 99 bearings, rotors and calipers. just below the 42 pin wire harness connector..... the wire harness can rub on the drivers side valve cover. wrap that in some rubber or something before it rubs though. never use dorman valve cover gaskets (uvch) , use alliant power or ford and never use anything but ford glow plugs. diesel o rings sells a schrader valve for fuel filter housing so you can check fuel psi. says not to leave it in but i have for 30k miles with out issue. i set my base psi at 65 psi with the fx fuel cross over kit. cannot say if that made any diff or not but if your pump starts to get weak and you drop below 40 psi you can damage the inj's. if the truck acts like it's running out of fuel at 1/4 tank then its the pick up in side the tank. easy to drop that tank.