Your aviary looks very nice, I'm glad to see this area recreated as to me it is the standout part of JP3.

Couple of things to note: I'm pretty sure the building the characters use to enter the aviary is supposed to be on top of the dome section, in fact it's visible in the final CGI shot of the aviary in the movie. I'm not supremely familiar with JP3's sets but it looks as if the aviary is actually extremely large and extends for quite a long way up the river, away from the entrance building. The pteranodon carries Eric away from the dome up the river, where you can see that the rest of the building (not the dome) seems to go on for quite some distance down a long canyon - I don't believe the opposite end of it is ever seen. The canyon part is covered by a series of metal struts with what looks like wire mesh between them. It looks to me that in your image you've made the "square" part end at a cliff just beyond the dome when the film seems to show that this actually goes on for quite some distance. It's hard to tell what's happening in the film though.
Is there more reference material for the CGI aviary than what is seen in the film? I'd be interested to know what the extent of the aviary is meant to be as it does appear to continue for quite some way up the river - the characters in the movie stay in the dome area (it seems as if the walkways are only present in this portion of the building), though Eric is carried a short way away into the "square" part.
Quote:
we don't see a crane
There is actually a crane or lift of some form visible in the top-right of the final CGI shot of the aviary, at the top of the cliff, and there is another pulley device visible right after the characters descend the steps into the aviary, and there seems to be some kind of control box on the wall behind them as well.
Here are some references:

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And check out the scenes where Billy is hang gliding or Eric is being carried by the pteranodon. The dome section isn't visible in any of those shots as it appears to be behind a bend in the canyon (the bend is visible in the first image I uploaded, behind the buildings - these shots are further up river (away from the dome), which means the pteranodon carries Eric further into the aviary and then Billy carries him
back to the dome part, where the other characters are. The "square" part looks absolutely massive in the flying shots as it is large enough to be able to hide the dome from view, and you never see the opposite side.
Anyway, not sure how accurate you're going with this, just thought it might be worthwhile in general to do some more research on this.

And apologies for the semi-decent quality of the images, I only have the DVD edition transferred to my PC. I have the Blu Rays with the free digital copy, but only ever downloaded the first movie.