Sounds like you have 2 debates here:
1- 4" or 6"
2- Is it worth shying away from 00-01 and/or a D35c
1- Start off with a the 4-4.5" lift, get it all dialed in, then add 2". It's easy and cheap to add the 2". I say this because if you are a noob at XJ's the jump from stock to 6" is a BIG one and can cause drivabilty issues if you don't have a baseline to start from.
1a- Do a 6" if you have deep pockets and are paying someone to do it.
2- No. The 0331 head issue is a lot like the D35c issues, drive smart and you will be fine (less room for dumbazz driving)