You are not too late. I am still working with the "mock up" engine block. For those who can not tell, this block still has the renix intake system which will not work with the Wrangler H.O. fuel management.
More importantly, I just found my solution for the alternator being so low and hitting the K-Member. The H.O. in my buddies Grand Cherokee has the alt just under the AC pump which brings it up almost 8 inches. I have moved to a new phone an as soon as I can get some pictures, I will get them posted to show what I mean.
John