Here is a more careful comparison up to catfish's stage. Currently Zero is ~160 frames ahead.
X route:
http://tasvideos.org/userfiles/info/70254910989155755
Zero route:
http://tasvideos.org/userfiles/info/70254895436613917
Just based on known factors, zero will lose 2 seconds to the 2 remaining bosses, but regain them on velguarder. In addition ~100 frames will be saved once I need to switch back to X.
So zero has to do the next 2 levels within about 250 frames of X to stay ahead. It seems almost doable, but my last attempt made it seem far off. I'm going to retry though since it just seems so close.
EDIT: I did a rough draft of X's climb in Catfish's stage. It turns out you also have to add a lot of lag to X's climb as well, it seems like VBA did not emulate this game especially accurately. He can still do it a bit faster then zero, but it's really not by much. I think not accounting for lag in X's resync is what led me to think that zero would be a lot slower, now that I am re-syncing and doing a direct comparison, zero isn't losing much time in Catfish's stage. he will still ose a good chunk of time in Hornet's stage, this is unavoidable, but maybe with enough work it will work out. At the very least, I have plenty of money in both runs, at this point it's basically a non-issue.