I'm jealous you have a khaki Jeep. Black and khaki looks awesome. What I did to get my letters straight was to mark with a dry erase marker where the bottom of the front and last letters were, then once I peeled the old ones off I was able to line them up pretty well. Make sure when you don't leave your decals in the sun while you're waiting to put them on, it'll cause that vinyl to get extra flimsy. I started with the first letter and once I had it seated and the contact paper was on I'd line up the last letter and slowly press each letter on one at time to keep the air bubbles to a minimum. It took longer than it probably would have but I didn't want to have to do it again. For the Jeep stickers I put the J and the P on first then did the E's. Hope this helps.
I apologize for the un-solicited IM. I was reading your notes about removing the Rubi stickers and replacing them with black. I'm doing the same. My LJ is khaki and Jeep using an offset color that is not appealing. With my black wheels, bumpers and other subdued changes, my Rubi, unlimited and JEEP stickers are all being replaced with black. Any recommendations for placing the stickers and getting it straight? I would appreciate any tips. BTW - I purchased my replacement decals from Pixel Decals, in case that matters.