Here is a list of parts that you will need. This isn't a complete list but it will definitely get you in the right direction. This is all under the assumption that you are going to use the stock NP231 transfer case that you are running now.
All of these parts/part numbers are from Advance Adapters website.
713087 or 713001-S -- Chevy V-8(bolt-in or weld-in versions respectively) into Jeep Wrangler engine mount kit
716693-AA -- Radiator 1987-2005 Jeep with GM V-8
50-9812 or 50-9808 -- GM SM465(2WD or 4WD versions respectively) to Jeep NP231 23 spline adapter
716055 -- Heavy Duty Transmission mount
716130 -- Master Cylinder Fitting for Jeep YJ Wrangler
716287 -- Land Cruiser Slave Cylinder Bracket for use with Chevy bell housings
716119S -- Land Cruiser Slave Cylinder
716119H -- Land Cruiser Slave Hose
716215 -- Metric To Standard Hose Fitting
715523 -- NP231 Shifter Bracket for use with Advance Adapters t/case kits only
You will need some sort of exhaust manifold or header. Advance Adapters has several to choose from depending on what type of head you have on the 350. I just used OEM ramhorn type manifolds but that is up to you.
To complete the auto to manual conversion you are going to need a few parts off of a donor Jeep that is/was manual. You'll need a clutch pedal assembly, brake pedal assembly, and a clutch master cylinder. You are also going to need access to a hardware store or a Fastenal because you are going to need some brass fittings and such to adapt a few fittings. You'll also need a bit of steel brake line and fittings to go from the master cylinder to the Land Cruiser slave cylinder flexible line. You are also going to need some adapter fittings to hook up the Chevy power steering lines from the pump to the Jeep steering gear box.
As far as the build goes. I started by removing just about everything in front of the firewall. Fenders, grill and all. Then I installed the engine mounts and then bolted in the engine. Then the transmission/t-case went in as one unit supported by jack-stands while installing the transmission mount. After that it was a matter of putting the front end back together and hooking everything up.
If you have any questions along the way, you can post em here or send me a PM.
P.S. Advance Adapters is running a sale this weekend.