[MENTION=119532]Road Bull[/MENTION]
I read this when you first posted it since I had the skids in my garage just waiting for me to have time to throw them on. My rig is a 97 4wd auto. I finally got some time today to get them bolted up.
I decided to just install them without removing anything or adding washer stacks. I figured if a had the same issue as you I could remedy it using your write up. After an hour of bolting and aligning the skids it was time for a drive.
I hit the highway and took it up to 85 with no noise or vibration. So far so good. Next was a well known dirt road that I like to drive way to fast on. It's been raining the past few days so the normal dust cloud was replaced by soft sand and lots of flying water. The skids also passed the dirt road test for my rig.
I got home and double checked all the bolts where still tight and called it a day. I did check the clearances from the skids the stock transfer skid plate as well as the dampener. Both had about 1/8 clearance all the way around.
So some people have this issue and some don't. With tolerances that tight it could be a number of things that make it fine for some and not others. I'm very happy with the quality and beefiness of the skids so far. Hope you are as well even with the issues you ran into.
Cool! Glad you got them installed without issue. Let's see some pics!
I am guessing most vibration issues are due to a new surface to old surface contact, (for example the transfer skid resting on new Savage skid / or transfer dampener contacting skid). Mine happened to be the transfer skid. I also think that you are right in your estimation of tolerance variables. These 3rd gens might have slightly different geometry for some of their parts from 1996-2002. For instance, I know that 2001 & 2002 have some unique parts that are not interchangeable with older models.
That, and mounts could be worn and so on and so on. So I can't say definitively that ALL 2001s or 2002s would have the same issue. But I at least wanted to put some information out there for the next guy so that he doesn't have to guess or troubleshoot a bunch of extra steps to get their skids sorted. I imagine that are many like you [MENTION=143526]theesotericone[/MENTION] that have no issue whatsoever. Hey... Did you have 13mm as well as 14mm bolts? I think all the bolts that fit into a threaded part of the skids, as well as all the front seemed to be 13mm, while the rear longer bolts seemed to be 14mm for me. Am I crazy or is that what you had?
The weather has been crap here, but I am still thinking about maybe making a short video about skid placement and order and known areas to check for contact. So maybe if we have a dry weekend where there is sunlight and no liquid sunshine, I might be able to make that happen.

layball:
If you're going from a stock skid to an aftermarket skid why would you leave the transfer case skid on? I would automatically think that the OEM skid would have to come off?
I didn't even really think about it till it was already done and buttoned up. Maybe this was because I was loosing daylight and maybe it had a fair amount to do with trying to get them into position without real supports, but more jerry rigged supports and using what I had at hand. lol.
I was kinda surprised that there were no directions that came with the box. For the most part, they really can only go on the one way, but because you start with the rear skid, it just feels a bit less obvious. When you get the bolts threaded, but not tight, it might look like everything will clear, but once you start ratcheting bolts down, it is difficult to see what is going on on the vehicle side of the skids.
It took some imagination to locate the source of the contact. I ended up taking pics of areas that I couldn't get my fat head inside. That, and my left eye is really just along for the ride and can't really see. So I was spinning around on the cardboard trying to find a place that I could get high enough to see the issue. After a few minutes of futile contortion, I realized I could get my phone into tiny places that I could snap a pic. That confirmed it for me. I knew that the OEM transfer skid was the issue. The harmonic dampener bologna was nowhere near my skid so I left it on. The only other thing I took off and left off was that ridiculous plastic splash guard that covers the fuel filter area. It seemed to be in conflict with the Savage skids. That, and I can't see it doing much.