you have really asked way too many questions to even begin on replying to them individually... congrats on the purchase, sounds like you got a good deal, 2-300 a month towards your truck is more than i've got to play with... you seem pretty eager to jump into it, but you need to slow down, take that much on, and none of it will get finished...
here's what i suggest you do, take everything you've listed, now prioritize it as to what you think should get done/what you want to get done first, and things that are not urgent at all... this list should be of EVERYTHING you might want to do, weather or not you think it's feasible, logical, or worth it long term...
next, go through that list and reorganize it to group together things that would be done at the same time, IE the 1350 to 1354 swap with any other work that requires the tcase to already be out...
next, search on this forum for any and all information regarding each individual task at hand, search google, and possibly a few of our "competitor sites" i recommend doing this task by task, you can work ahead of yourself, but chances are you'll forget what you read, by the time you get to working on the bottom of the list...
james "jim" oaks owns TRS also, so i won't say anything bad, but body lifts are everywhere, make sure you're getting the best price buying from him... IIRC when i bought mine, bodyliftkit.net was the best price i could find... additionally, make sure you buy from A) a trusted seller, jim would constitute as one of these imo, and/or b) a brand name you trust (i used performance accessories because the reviews and sales were off the charts)
also, i am not implying or saying that i believe bodyliftkit.net is a trusted seller, i do not have any experience with them, i did not buy my lift kit from them, i used them for price comparison only, they may or may not be a good site to deal with, i take no responsibility if you buy from them and get scammed or if they rock