Good list mate, bit bloody expensive and I'd bet my left one the truck will be off the road longer than you anticipate even doing it yourself, so just keep that in mind to save further frustration (mine was out for 11 weeks in a period of 17 weeks!!). That equates to a lot of coin also, but choice is yours. I'm sure you've done your research but a quick ballpark below:
1. After market ECM - between $1600-$2100
2. Reco, balanced efi engine - $2000-3000 minimum for a rebuilt one (probably more like $4000)
3. molly rings - $??
4. oil cooler - $250
5. lower comp - machined head $1200 or decomp cylinders $2400
6. larger injectors - $480
7. Performance fuel pump and reg - $280 for pump and $? for regulator (don't know if you'll need it though depending on what ECU you get)
8. tuned pipe header - $500-600
9. twin pipe dump for better flow and reduced lag - $300
10. Garrett turbo water and oil (assuming you mean water and oil intercooled) - $1500-$1700
11. twin electronic turbo controller (why twin??) - $540
12. intercooler with recirculating pressure relief valve - $700
13. egt sensor and gauge - $150
14. Knock sensor monitor - $250
15. pcv catch can (second hand???) - <$100
16. most pipe work and mods done at home - fair enough if you know what you're doing
17. head de-comp and both ports smoothed out - as per point 5 above
18. engine and most pipe work done prior to fitting into car and up and running - if you can do most, not much in service costs, but maybe allow $700 for dyno
That is a big expensive list mate!!! $12,250 on the cheaper side of every point above and not including dyno. Will be following your build with great interest - please post updates as you go once you decide which way you're heading. By doing the work you've said yourself, you'll be saving at least $4-5000 in installation ... sincere best of luck with it.
Bound to be a bottler!!