IS your bike a EFI if so the Fuel pump is the noise when you turn the ignition. So if that isn't pressurizing the system you would have no fuel delivery, That might explain the missing etc. The top end noise could be associated with the same fuel pump problem. Pull the pump and see what the go is. You can short out the pump relay so that the pump runs all the time, that will allow you to see if it is the pump that is stuffed.

Crimp
What year and model bike. Does a warning light come on the speedo when you turn the key on . Harleys have a self diagnostic system so we need to find a fault code. Are you saying the bike has no compression ? Like a leaking head gasket. Does your motor have decompression releases.

Unplug the powercommander and run the ECM straight up. My old superglide died when the PC3 took a dump.

I don't know much about the PC5 but taking it out of the loop with the problems will discount that. When you turn on the ignition the pump should be quite audible as it pressurizes the system. It should run for about 2 -3 secs then cut out. The engine check lights remain on for a further couple of secs then go out, If the engine check light remains on then you have a fault code. As you have said though no codes. The fuel pump is electronic so be careful looking at that if you have to. If it is the pump the first thing to check is the filter on the pump as they can cause all sorts of issues if they become blocked from a bad batch of fuel.

Crimp
After reading this post again. Did the motor start vibrating any worse than before. The top end rattle with the motor not running under 3000 rpm sounds terminal to me. Maybe pull the PC and have a dealer check it over in case she scissored the crank. HD might still come to the party as long as the PC had nothing to do with the engine problem.
Good luck.

Great news
If the PC is stuffed it's better to not run a piggy back tuner because it's something else to fuck up on the bike. Consider a TTS, SEPST or a Tmax with its own ECM. Welded crank sounds like a nice engine build ?

Luck of the draw as some PC's last years and some don't. it's hard to beat the stock ECM for reliability. With your motor build it's best to pick between the TTS and the SEPST because it's a touring bike and there's shit fuel around country Australia. The stock ECM has knock control that adjusts the timing to stop detonation from crape fuel. If your a hands on guy you won't beat the TTS on a modified engine for a home tune. If you want to get it dyno tuned ask your tuner what unit he prefers to work with and go from there. Remember There's good dyno shops and bad so do your home work on who to use. My personal choice for the TTS is Steve Wacker from Morgan & Wacker Brisbane because he was trained in the states by Steve Cole on the early SERT (TTS). He's not cheap but spends 8 hours building a custom map from scratch. $600
HB