It may be a pain to find the stock parts, seems like most people who are modding SHOs keep the stock parts as well. I have my stock airbox, but am keeping it, and will keep my stock downpipes as well. I also kept my stock mufflers/resonator when I welded in replacement parts.
LME tunes are good I heard, but I really despise how they went away from SCT. I like the unleased tunes a bit more because you can datalog. I run a tune form a forum member on one of the ecoboost forums, who tunes on the side, and does dataloging revisions from the start. I am running an E20 blend with him and it is amazing. The HPFP will be a great option, but also pricey, and still will need a few other things to be able to run full E85 all the time, I believe.
The biggest issue with your option list, is the moonroof-delete. I phrase it that way since almost all the SHOs I have ever seen have one. I ordered my SHO new to my build specifications because of the options I wanted.
How do you like the JLT? the can is smaller than the other options (UPR and RX) and no clean side seperator, but also much cheaper. Not sure which to go with, but will be getting a catch can soon. I just installed my 170 Reische Thermostat recently, and am installing my catless downpipes next week, as well as finishing my A/F gauge install. I also am installing my hotpipes soon.