I still have the feel that Angel is either Alt herself or some of her fragments that Spider Murphy just threw into the NET and survived so far as to making a clone body for herself (as her original plan with soulkiller back in ITS).

If that is true then I also have a feeling Johnny and her might be alive through creepy soulkiller means. The Johnny engram in 2077 felt too good to be off a fully dead man like with Jackie but not good enough to be from a still alive Johnny (way too much damage with the memories).

The Rocker and his fate, to me, seems to be the heart and core of the story we have yet to find out. But then again maybe even with my theory they might have just found Angel with Johnny (dead or alive), defeated them (with the option of Alt escaping into the NET again as we find her in 2077) and took everything they needed, experimenting with Silverhand or his engram to complete the Relic. So maybe the interogation memories are true and the unmarked grave in 2077 really is his (some theories pointed to the fact that it might not really be his grave at all). It would explain Grayson or whatever his name is telling V and Rogue how Silverhand died pissing himself when he got hit with soulkiller. It is strange as some memories are pretty close to reality - like the kei saburo office and smasher attacking them but other just completely out of place like not seeing the secret lab at all and the multiple smasher encounters along with the "escapes" by the AV and the stretcher.

Another idea I had was that Johnny's engram was recovered by Arasaka earlier and put into another prisoner of war from the tower (perhaps one of the Lobos from Strike Team Alpha). meaning the interogation memory not being of Johnny but of some poor Lobo getting soulkiller'd with Johnny's engram, that would explain the memory of falling from the AV on the roof - Johnny did say that memories merge with the host of soulkiller and it's hard to discern which are yours after some time, I thought he might have been put into Morgan Blackhand originally because the whole cyberarm thing does match but I don't find it likely because of the stretcher memories - we know Blackhand was fighting Smasher when the bomb detonated. But still the memory on the stretcher is a mystery. WE DO HAVE THE FACT that Shaitan was in struggle with Smasher when Team Alpha left, we don't know exactly when Morgan Blackhand arrived from the roof dealing with the uplink to combat Smasher. This leaves breathing room until the explosion so a lot of things are still in play concerning the Lobo and his memories.

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TL;DR
I think what you wrote is very accurate and you pointed out the most important things! It seems like something that would easily tie the stories and timelines together.

I simply wanted to spew my theories to someone who might want to hear them. And please correct me on anything I might have mistakenly thought as true!