Dan,
I sent you a pm with rockjocks info.. he is local and knows all the suspension options for these trucks. As mentioned above there are the guys in PHX area which are also very well respected if you can get the rig up there. After looking at the work and reviewing some corrections on what has happened I think there are a few things that can be attributed to the work and others possibly not. AS an aside most of the guys on this board wrench on their trucks, use only known LC shops or find themselves learning the hard way. Guys here wont even take their rigs to Toyota dealerships. These trucks are bomb proof but do require expertise which unfortunately you wont find everywhere for 1990s era vehicle even at Toyota.
Some responsibility does unfortunately rest in your hands. In this case you asked a guy to do a lift on your truck and only seemed to give him one condition, price. His work is definitely not elegant and probably no one on this board would accept it for their rigs, but it does accomplish a lift. A lot of guys run spacers on the top of their springs to net higher lift so in some sense this is another options, albeit not well used and/or accepted. Im not defending the guys work, however, its always best to have all work written down prior to start. If something is done that you didn't sign off on then take back the truck. I realize you may not have been a technically oriented person but you could have googled landcruiser lifts to get an idea of what was available and general costs. You will probably see that a decent set of springs and matching shocks for the LC ( 4 ") + install is hard to find for $1000.00. Seems this guy may have ordered what was available close by and inexpensive and did custom work to compensate. It also looked like he lengthened the stabilizer bar brackets if Im not mistaken. Im not sure what else he did as the pics aren't terribly well positioned. As for the trunion bolts this is a know issue on some rigs and has been recommended for everyone to check periodically! The vibes were probably created by the lift- Lifts over the 2.5"-3.0 are known to create vibes in many cases. Also worn out bearings and an older vehicles= noise, especially after a lift. Lifting older vehicles can exaggerate problems you already have so just be aware his work may have only helped to identify problems you already had. Getting someone with experience to look at your truck is worth the $. Trail boss doesn't sound like the place to go given their use of terminology.
It would be helpful for you to summarize where the $5K you spent went. You said $1K for the lift. $4K for exhaust work and ?.
If your looking to drop in new axles I will have a set avail. non-locked. Also there were two guys on the local CL that were parting out.