Let me tell you my similar experience i went through recently that might shed some light on your situation.

i race my dart regularly, it's now a 408 stroker, but at the time only had a 318 that would push the car to low 14's. the tranny was rebuilt and i purchased a 3000 stall B&M converter when it went together..(also i'll point out that a 3500 converter for the street is completely fine...i drove a 4500 to the track every weekend for years without a problem, flash speed and their advertised stall speed are very diff things) any ways, on a pass down the track (on motor) i lost 3rd gear completely, shifted into first, second, every gear but drive. i checked my linkage a thousand times, adjusted it slightly and it appeared to fix the problem...for a week..then it did the same thing...i called my trans guy and gave him h@ll about my 1000 mile tranny blowup i just had.. like your guy he said he'll go through it for free, but also said that my pan full of shavings was most likely a blown converter. i thought he was an idiot until i went to pull the converter off of the pump. the converter had internally blown up and basically ate the front of the pump shaft off..these shavings then clogged the valve body, which restricted pressure for the shift. long story short, i apologized, gave him his deserving $250 for the rebuild and intense cleaning my tranny needed...and then proceeded to call B&M and give them hell instead. they basically said it's out of warranty, i'm on my own, and i basicaly said i'm done with their crap and my next one will be a TCI with an anti baloon plate.
long story short, neither the trans builder or the converter company is gonna own up to it. i know nothing about boss hogg and i work for what we'll call...(americas #1 performance warehouse)..they might be good, no idea...my mistake was running nitrous on a garbage $300 converter, i felt no shudder, shake or anything, and had no idea the converter went until the valve body clogged, also probably only made 20 nitrous passes on the motor, and it had beena bout 5 months since the last one...so learn from that as well..and back to your problem, your tranny builder seems very unprofessional..loose bolts? come on..but that would just cause pressure leaks and stop you from shifting..the other parts found in the pan show his parts failed, either as a result of the converter going, or on thier own....i'd be leaning to his fault since now he also gave you a seized pump, and i'd be the first person to blame a budget converter, but in this case i think it's on him, and the converter and trans both need gone through. if there's shavings in the pan, there's shavings everywhere else. if the converter checks out ok then again better business b this guy...hope my long winded story and opinion helps you.