Having weird running issues with car

Alright guys so I am having some really weird problems I cant get to the bottom of. So this all started last saturday, my car got rained on, whatever, go to drive it home from work and its acting weird, its running rough, and bucking nothing too serious though, I figure something just got wet. I was planning on going to the track next morning, so I wake up next day driving to the track everything seems to be running fine. Go do my first run, everything seemed good, ran a decent run, park at the pits. Moving up to lanes to go for another run and my car is acting weird, the engine is surging and the tach is bugging out, its jumping all around, obviously not following the actual rpms of the engine. I was already lining up so as I go down the track it was obvious the car had no power so I coasted through and parked it to see what was wrong. Started moving stuff around and felt the distributor bolt was loose, really lose, so I figure ok my timing just got out of wack. With no timing light on me I just adjust the timing by ear, cut my losses and drive it home. On the way home it was running realll bad, had no power at all, but I knew I needed to put a light on it and fix it. So while its parked in the garage I installed a bigger throttle body I just got in the mail, and also set the timing to 14*, cleaned the threads in the block and put a new bolt in there since the old one was buggered and suspect that was the reason it was loose.

So, I drove the car to work today and it just runs like complete . It really seems like the timing is off but I've checked it again, distributor is tight, and it hasn't moved. Above 2000 rpm the tachometer keeps bugging out, and the engine just sounds bad, it sounds like a truck, it really sounds like the timing is off, when I let off the gas it back fires, loud pops out of the exhaust. Also putting it in neutrul and coming to a stop the idle drops down reall low almost stalling, I have to give it gas when coming to a stop.

So I guess I messed up by putting the t/b on without fixing the problem first but I really thought it was just a timing issue. So here are the things i've done, I've check the codes and the only ones I have are emissions related from removing the smog, and egr. I also have a code 67 (bad neutral safety switch) but I heard not pushing in the clutch when checking codes or having car in gear will cause this which I did both. Also checked plugs and they look dark, not fouled or any build up but dark orange. Also opened distributor cap and found small metal shavings on the inside of the cap, hard to even call them shavings they were so small. And, the rotor button had weird black powder on it.

Other things I am suspecting that can be wrong, my MSD 6al box? I have an MSD coil could that be bad and cause my tack to act funny? I also am going to check the TPS since I just installed the new t/b but I did not get a tps out of range code so I dont think that is it. I also am going to take my ignition module into the parts store tomorrow to have it checked even though it and the distributor are brand new. Sorry for long post, I am almost out of ideas, I am about to take the valve covers off and see if anything is wrong mechanically in the motor...