Phase four of the project.  The 231 V6 is done and all the quirks have been worked out. Placing the engine in the frame with the tranny and T case married together, the Skyjacker T case lowering kit is in and done. Then we go to weld the new motor mounts in and get every thing allighned where it needs to be and notice where the engine is now, looks to be at way to much of an angle it is possible that the fan could hit the fan shroud. Now the T case lowering kit was advised because of the 3" BD lift that was put on it.  Now we think that if the T case lowering kit was removed it may level itself out. Also the original installment "guide" from Novak had mentioned something about moving the engine forward and to the left, but that was to fit the same motor into a Flat Fender not a CJ5 It is hard to follow because the frame of a CJ5 is different. Any info on this will be helpful in solving the problem. If I am not clear on something please let me know. Sorry for being long winded.  

Engine placement for a swap is all about clearance. Off-setting it to the right gives some clearance for steering components. Forward gives some tunnel clearance. The powertrain should be level as a starting point. The powertrain angle should be adjusted for optimal driveline angles. The rear output of the TC should be inline with your diff. Off setting for steering an inch or less is fine. Set the motor mounts higher to decrease driveline angle, don't lower the TC. Pay attention to hood clearance when doing so. Plan for a fan shroud. It will make or break your cooling effectiveness. A wider fan shroud can be trimmed for propper shroud clearance, but too narrow and you're not shrouded. Propper fan clearance is front edge of fan 1 inch inside the shroud and no more than half the fan depth inside the shroud. If you pay attention to shroud selection now it could help you with engine position. I'm guessing BD means body lift? That's good for clearance issues. Why the TC lowering kit?? The tranny mount should be designed to acheive optimal driveline angles. Make sure your exhaust header/manifold is on and maybe even have your head pipe built hugging the motor as tightly as possible. Oil pan clearance with front axle (fully compressed) should also be looked at. Two things to get you out of a tight spot (pun). Consider Borgeson joints for your steering joints and a double cardin drive shafts.  

thanks for the info.  The BD stands for Black Diamond suspension lift and the lift is 3 and 1/2 inches that is why they recomended the T case lowering kit I guess I can move the motor mounts forward to gain a little more clearence and level it up a bit more everything is free so it can be easily moved until we find the sweet spot. Any more info is great thanks!  

Transfer case lowering kits are to improve driveline angles when doing a  suspension lift. You have the opportunity to set your driveline angles the right way because you are setting the drivetrain.

In your case, do not use it. Read up on drive shaft angles before you determine your final drivetrain position. Determining driveline angles is one of the steps. And an important one. Your solutions will rely on motor mount height, tranny mount height, cross member design and rear axle housing rotation.

Shimming the spring pads might be part of a solution. But they should only be used for a slight adjusment (1 or 2 degrees). More than likely your solution should be to remove the spring perches, rotate the housing and weld on new perches.

There is a lot of info on this subject on the net. Search and you shall find.

Pay attention to the front driveline angle also. Not as important as the rear, but will change with any adjustments.  

Here's some reading to start with:

http://www.4xshaft.com/tech_slopesVSangles.html

http://www.4xshaft.com/driveline101.html  

Thanks for the info one more time this will be helpful. This is my first vintage build and anything can help me out. I have gotten a lot of help all over but it does seem difficult being that most only know about the newer jeeps and not about the old. JP mag has helped out even though Cappa has thrown the CJ under the bus in recent mags. Thanks again!  

Cappa didn't really throw the CJs under the bus. He just thinks there are better foundations to build upon, if given a preferance.

He's a vintage guy. He likes the old stuff too...  

Well then I guess an apology is in order, I guess my understanding was that Cappa was not holding a CJ in a very high regard.  Reading what he wrote in the magazine told me and a few other readers that I know that basically CJ's were just rust buckets and you could never really make a good 4 wheel rig, and that most people should have newer Jeeps if they really want to "get after it".  So I won't take it to heart but maybe they should all come up to Montana and do a little wheeling.   Because what they will find out is most people that get after it, prefer the Vintage stuff too.  So disregard the "smack" because I know he gets a lot of it!!   And thanks again for the help....now off to the shop to figure this bad boy out!