Alrighty here. You guys are getting a little too excited and thinking past things.
Ideal links for strength and scrapage. Use TUBE, not pipe. Tubing is measured by OD, pipe is ID.
1.5" x 0.250 wall DOM sleeved with 1.75"x0.120 HREW. I have tubing adapters that will fit in the 1.75"x0.120 in both LHT and RHT for 1.25" heims.
This way your link isn't rediculously heavy, it will take a beating, and it won't be so large that it gets hung up on everything. I've been running those exact links in the rear of mine and everything is fine.
If you are interested and know the lengths, I can build the links with tube adapters, jam nuts, heims, and misalignment spacers for you complete for a good deal.
As for hydro. I only know of one supplier that can get RTC hydrostatic steering units. They are around $500. If you are running full hydro, your stock pump will be able to handle it (at least mine does with 38s). You need to figure out how many turns lock to lock of the steering wheel you want to pick out the correct steering unit. You also need to know the range of motion the tie-rod has from lock to lock in order to get the correct ram. I can put together a full hydro non-RTC kit without brackets (they are different for everything) for around $950.
People have mentioned link seperation and what not. It is important both on the axle and chassis side. It isn't as simple as making some links, welding some tabs on and bolting the links in place.
You have to figure out what design is going to limit your articulation steer, maximize your flex, and do this while keeping your anti-squat and instant center all within reason and while working with the tolerances of your chassis. There is no one way to do it, but it would be in your best interest to figure it out before you start building anything. Link length and angle (x,y and y,z) play a factor there too.
As for the Atlas, they only make a right or left hand drop. From my understanding, the rear 404 axle is centered and the front is offset to the driver's side, so you should have nothing to worry about in terms of driveshafts lining up.
Now, the crawl ratio.
If you have and auto, you will be better off. First gear in an A4LD is 2.47. Your 1354 case's low range is 2.48. The 404 axle end up around ~7.56 with the hub reduction. That would give you a crawl of around 46.3:1. The TQ converter would (on average) double that to put you at 92:6.
Now, if you have a 5-speed, you are in worse shape (IM0). The Mazda 5-speed has a first gear of ~3.9. The t-case is still 2.48 and the 404 end ratio is ~7.56. That leaves you at 73.5:1 for your final crawl ratio.
For comparisons sake.
I run a 4.0, C5, 4.3 Atlas and 5.13 gears. That puts me at ~112:1. I am running 38.5x14.5 SXs and I will tell you that it isn't enough. I need either lower gearing (my only option is the 5:1 gears for the A2) or more power.
So what does this mean to you? It means that if you are considering running anything bigger than a 37 with the current tranny, t-case and the 404 axles (which you are) that you are going to have to get more power or lower t-case gears, or even possibly both.
A 4.3 Atlas with the A4LD would put you at 159:7. I'd say that would be good for nothing larger than a 42. If you have the 5-speed, it would put you at 126.7:1. I'd say that woul dbe good for nothing larger than a 38.
A 5:1 Atlas with the A4LD would put you at 186:1. I'd say you could run nothing larger than a 44 with that. With the 5-speed you would be at 146:1. I'd say that would be in the 40" tire range.
Those are just tire sizes however. The bigger and wider you go in tire size, the heavier they get and more power/lower gearing they require. Therefore those tire sizes may need to be dropped by 2" per selection.
If I were you I would also plan on getting an Atlas 2 right from the start. I also think the 42" tire would be ideal.