Yup, you're probably best off going to RC Crawler for advice, but I'll give what I can.
For the gear ratio, you don't *necessarily* want the absolute lowest you can go. Do a bit of research, but it's sometimes useful to have a bit of wheelspeed if you need it to get over a stubborn obstacle. You're looking at probably 40 or 50:1, but like I say...double-check with the pros. It depends on your motor, of course. Tyres need to be large, fairly narrow and above all, soft with plenty of sidewall to flex on. Perhaps even put BB's in the tyres, to improve purchase.
In terms of axles, there should be a variety out there. Your dimensions seem pretty small, but perhaps the Losi 1/18th crawler axles would be of use? The most popular class by far at the moment is 1/10th so your choices are limited, but either those or maybe TLT axles would be useable. The TLT ones are a bit outdated and larger, so I'd check out the Losi ones. You'll need to use some kind of sliding driveshaft., and the classic 4-link suspension (triangulated top links to stop the axles moving out of place). You could perhaps bend the lower links to increase ground clearance.
60 to 70 degrees of articulation is about what you want; any more, and you'll probably run into binding issues and it'll just tangle itself on the rocks. Do you need to use cells that you already have, or can you buy new ones? It's just that some 2/3A cells would be perfect to mount on the axles (the type that are used in 1/18th vehicles). They don't need to be high capacity for crawling, and less weight is always good...but any that you do have, you should try to concentrate on the axles. A 540 motor sounds a little large, so perhaps there are small options out there? You'd have to research into that.
Other than that...just try to keep everything as low as possible, while keeping high ground clearance. Keep the chassis strong at its link/shock mount points, with plenty of cross-bracing for rigidity. And soft springs, with the suspension set so that the shocks are only about half- to three-quarters-extended at rest.
That's all I can think of from the top of my head, but the RC Crawler guys REALLY know what they're talking about. You'll get all the help you need there.
