Chevy V6's are hard to put into these Jeeps. We have had some installers be successful with them, but it took a lot of work.
Dustin is right. Using a lower profile Chevy V8 is easier and because of the availability of low-profile accessory kits for the V8's versus the V6's (let alone the power and performance advantages), I'd sure nudge you in that direction.
Note that this comes from a jeeper with an LU3 V6 in my CJ. But because of the high hood, they fit like a champ.