Sounds like you did the same mods I am looking at, did you have to use a sye to start or can I get by for a little while?
You can get by just fine, I'm at 3.25" suspension lift and didnt do the SYE, I didnt even do the transfer case drop, I did however eventualy do the motor mount lift and associated body lift of 1.25". As for the Dana 35c rear, I run one, with a 2.5 your not going to put huge amounts of strain on it unless you go up to 35" tires, with 31"s your fine as long as your not a huge throttle jockey type driver off road, when I switched from 31"s to 33"s I made sure I had alloy shaft in before the tires went on. I wheel pretty hard, but not throttle heavy, another inexpensive upgrade you can do is the D35 truss from Superior. Yes, a lot of people will say its a ticking time bomb and dont waste money and make you feel you need to get it out of there right away, reading what others said like that had me worried for about a year, I had access to a guy who builds a lot of bolt in 8.8" ford rears, when I found out the 8.8 is also a C-Clip shaft just exactly like the 35, I started looking at c-clip eliminators for the D35. Where you get in trouble with the D35 is having a 4.0 and being throttle heavy, or having too large a size tires.
Before next season I'll probably go up to a 4" non-progressive lift, at that point I'll do the SYE, if your driveline angles arent bad its not a huge issue, and mostly until you get in to very large lifts it isnt an issue. This is a link to Tom Woods website, at the top click "tech info" and it will show you good and bad driveline angles.
Tom Wood's Custom Drive Shafts - Tom Woods Custom Drive Shafts Custom Driveshafts Specialist
I'll be regearing to 4.88 myself, I'll get them through Rough Country, they sell Motive Gear products and for under $500 I can get both ring & pinions and master install sets for both axles in one kit.
Do a lot of reading and dont believe everything people say in forums, including me
what works for me might not work the same for you, it all comes down to try it and see, you get good advice here, but keep in mind that advice is based on their Jeep and experiance and driving style and variables, you will always get a different result because your a different person with a different Jeep. Still, the majority of people will try to be helpful.