If you keep the planes equal so the u-joints are lined up properly you should be able to get away with it. How high are you going? You might be able to get away with stock t-cases if you slide the rear axle back.
Great. I actually lowered the case appx 2.5" while keeping the same angles. I also built a frame to protect the case should I pyramid. Further down the road I plan to run 35's so I feel the sacrifice of a lower belly is worth the trade-off. Im mainly after water clearance and flex.
My trouble started with 4x YJ's and 4x missing links. Full droop was not quite enough for the u-joints. I lengthened both drive shafts and removed the existing spacers I was running (pre YJ). Thx for the responses.