Most perplexing, and most frustrating.
As a general comment, first on the list is anything touched or replaced as relates to both ignition and fuel, although my guess is that it's fuel related and not ignition - other than the potential for wrong high tension leads to plugs connections.
The TPS is a good check, but unless it was visibly damaged, I'd rate its involvement as being a lesser probability.
Injectors laying dormant for 14 + years are instantly suspicious, especially if never inspected or cleaned.
But something else strikes me as being worthy of investigation.
The FI system is very reliant upon MAP.
And whacking the throttle really jumps the vacuum level about, while small throttle movements don't.
So, on that basis, I'd be look very carefully at all the components that pertain to MAP, meaning not just the MAP sensor alone, but also all hoses and wiring plus their connections.
Another thing, the 2002 Cali' bike "smog stuff" you removed is a carbon canister for fuel tank vent gas.
Be sure you have proper venting for what is now an altered system that no longer has a vent gas canister.
Good luck to you !