Keeping it challenge priced would be a pretty hard challenge but not impossible. I swapped my z31, after selling the engine/trans from the car and the extra parts that came with it, for just a hair under $3000 which includes the price of the car itself, I wasn't going for challenge budget but was trying to keep it low cost. That was also a bone stock truck engine with no power steering.
Your questions still seems too broad to get a true answer. With basically every LS engine having mostly interchangeable parts it's hard to answer. I can give some general insight from my experience.
With swapping into a tr4 i'm guessing space will be tight. z32 5 speed trans can be had with an adapter plate and have a smaller body/bellhousing to them. might be able to keep from having to hack up the trans tunnel too much. The starter is also off the side of the bellhousing vs. side of the block which helps free up some engine bay room but might interfere with the passenger footwell.
You can see where the LS bellhousing bolt pattern is vs. the nissan pattern
Also stock manifold have a whole slew of different collector locations and are cheap as most people just throw them out when they swap to headers. They also might not flow as much as headers obviously but they still flow pretty well for factory.
LS3 camaro have a decent rear, straight down dump on them.
Also c6 non-z06 vette manifold have a pretty tight, high up, center dump
Also car intake manifolds are nice and low profile and help to clear low hoodlines but truck intake manifolds flow better, specifically the Trailblazer SS intake. Depending on the intake/fuel rail you use you might need a returnless system. That can easily be done with a corvette fuel filter, it has an internal regulator and a return line from it to go back to the tank, then you can run the outlet of the filter to the fuel rail and be done. you can see the inlet and the return on the bottom of the filter and the outlet at the top going to the fuel rail.
There are 3 different accessory spacings as well. truck, car, and vette. There are companies like ICT Billet who make dozens of different accessory brackets to pretty much put any accessory in any location with any spacing although they can get pricey.
For oil pans you can find basically any of the dimensions you'll need online, atleast for factory pans. as far as i know any pan can fit on any engine with the correct windage try and pickup tube.
Also if the Indy part of Indy-Guy means Indianapolis I live in Columbus, IN and have a few LS and misc. parts that I'm looking to sell if you're interested at all.