Why didnt they get the two male survivors to ID Allen earlier?

Pretty much everything about the "zodiac" investigations was shoddy police work. No... literally... everything. Yet Dave Toschi is somehow romanticized as a good cop. They basically ruled out dozens of suspects on handwriting alone, only to discover that he probably traced most of the letters from other people's writing. They also ruled out people because the miscellaneous bloody fingerprint in Paul Stein's cab didn't match their suspects? It doesn't take a genius to figure out that this guy was highly intelligent and invented ways to fool the police.

Well Hartnell couldn't have identified Allen by sight because the guy who stabbed him and killed his girlfriend wore a mask. That leaves Mike Mageau and in the movie they make it seem like he moved away after the attack and was hard to find. I also think that in reality the cops were never real gung ho on the idea of Allen. They only find out about him in IIRC 1970 or so when Don Cheney tells them about the comments that Allen supposedly made. And they make some attempts to investigate him afterwards but never seem to press too hard on it. I think that Allen is much more of a suspect for Graysmith, who fingers him because of a lot of circumstantial evidence (Allen owning a Zodiac watch, his timeline kind of sort of matching that of Zodiac, his possibly knowing one of the victims). By the time they show Mageau making his identification of Allen, Graysmith's book on the Zodiac would have been published and would have had much more of an impact on thinking about the case.

Unless Alpert's covered in bacon grease, I don't think Hugo can track anything.

It wouldn't have mattered. Just about all of the information we now know has made it clear that Mr. Allen was not responsible for the killings. From http://www.zodiackillerfacts.com/allen.htm

"Fingerprint comparisons, palm print comparisons, handwriting comparisons, and DNA comparisons appear to exonerate Allen, and more than three decades of investigation by police, the media and amateur sleuths failed to produce any credible evidence to link the so-called "prime suspect" to the Zodiac crimes."