For the injectors, in '03 the spec was 24 ft-lbs, later they increased it to 26 ft-lbs, and most builders recommend 28 ft-lbs to ensure the copper washer seals well. Make sure the bolt holes are clean and free of oil as this can affect the torque.
The rail bolts are 8 ft-lbs (96 in-lbs) for my '03, and your '04 should be the same. There is a sequence to tighten them in, here's the diagram from my service manual:
Tightening those oil rail bolts made me very nervous, being aluminum, be very sure of your torque wrench accuracy. Also, I just did 26 ft-lbs on the injector bolts, since that was the higher of the two factory specs and I didn't want to break anything. Good luck!
Driver or passenger side? I did both, and if I recall I couldn't get the torque wrench in on the lower passenger side so I used a box end wrench and did them by hand, comparing with another bolt I had torqued to about 85% of spec.
I didn't bother cleaning out the injector bores, I was concerned about knocking pieces of crap loose in there that could interfere with a seal, so unless you have the cleaning brushes and do it really well I wouldn't do it. Most builders use clean engine oil or ATF to lube the new o-rings, I used clean motor oil.
Not that I know of. I have smaller wire brushes that I put into a drill bit extention that goes into m 90 degree angle grinder. I put it odwn there, give it a few turns, spray some BG carbon cleana nd wipe it clean with rag and screwdriver. Than I either use my Blue-Point vacuum and suck the cyliner or blow it out with blowgun... Usually both. I then take snap-on camera down bores to make sure we all good... and pick up some STP Oil Treatment... Its thick as #### and it great for seals
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