I will reiterate kudos for asking BEFORE you make a blind leap into a costly mistake!
Coke versus Pepsi, this is a very good analogy. There's probably no 'best' engine, only the devil you know and love. The whole mechanical versus electronic comparison usually relates to those who turn their own wrenches because with at least a basic understanding of diesel engines any mechanical issues is just that - mechanical. But as soon as you add a computer to the equation that gets much more complicated and often expensive. Electronics also limit your ability to do work yourself unless you're willing to spend thousands on diagnostic machines to troubleshoot those electronics which means now you're at the mercy of a diesel mechanic or *gasp* dealership. So I think there's two questions you need to ask yourself:
1. Am I going to learn to work on my own diesel equipment?
2. If no, who am I going to take my diesel equipment to for work and what models do they know well?
If yes to #1, stay as mechanical as possible and deal with the age and rust that usually accompanies that era. Try to get something from the southwest or Pacific Northwest which usually see less rust than Midwestern or east coast. Prepare to spend more for these and plan on having it professionally inspected BEFORE you buy it. If it's roadworthy plan a nice long slow maiden voyage home, anticipating not everything is going to be new car perfect and it may need to be babyed that initial trip.
If #2, the basic rationale is whatever your mechanic knows well, buy that. If he/she's a whiz with Navistar engines, look for ICs which are mostly IC/Navistar engines. If the mechanic is leery of CAT engines but you have your heart set on a bus with a CAT, just be aware your mechanic is going to either shy away or drag feet or spend way too much time researching because that's not their forte.
As for transmissions, well there's not a lot there to discuss, it'll be whatever comes in your bus. As long as it's not an AT545 you should be fine for most any build out. If down the road it's not up to the task a transmission swap is totally feasible but not cheap. My personal philosophy with transmissions is run them until they die because the cost to repair or replace is about equal. That's just me but I've never had good results from rebuilds.
Hope this helps and good luck!
This is all spot-on tips and info.
My choice of the 06 DT466e with EGR came down to a few things. First, that's what I standardized my party bus fleet on based on the recommendation of my mechanic friend.
His first choice would've been a fleet of 12-valve Cummins, but you can't get those on an IC and I had ruled out BlueBird because where I live you can't get Bluebird OEM parts quickly or easily which we tended to need more than Cummins OEM parts. International dealers are a dime a dozen. Plus (at the time) he was a mechanic for one of those International dealers and could pickup my parts on his way from work...
So his second choice was the Navistar 7.6 which is what we bought a fleet of. He actually prefers the 2004 and older without EGR but was more than happy to teach me how to "permanently fix" my EGRs

So when I sold off the party bus business and fleet and bought my conversion rig, the 2006 IC CE300 with the larger 245HP 7.6 DT466e and the bigger Allison 3000 is what I bought. Took forever to find but I don't regret it for a minute. I could've done <04 without the EGR, but those were on AMTRAN bodies that rattled and have extremely unreliable dash gauge clusters lol. "Fixing" an EGR was easier than rewiring an entire dash in my opinion - plus I like the curved looks of the 05+ IC body.
The point about expensive diagnostics is spot-on. Fortunately Navistar makes ServiceMaxx available for free for pre-Maxxforce engines so a cheap laptop and a NexIQ (not exactly cheap unless you go the Chinese knock-off route) makes for DIY diagnostic capabilities that you just can't get on Mercedes, Cat, or newer Cummins without getting Chinese knockoff software. I can't spit on the Chinese knockoffs too bad - I use a Chinese knockoff version of Allison DOC to tshoot my transmission.
Over the past several years my friend has taught me a lot - I went from being a computer nerd who could barely replace a battery in my pickup to being a computer nerd who is able to diagnose and do most simpler diesel repairs. My mother is still astonished. :biggrin: I draw the line at opening up the valve cover yet, but my friend tells me I've seen him replace enough injectors that I could do it myself. There are a ton of good YouTube resources as well. A willing attitude to get dirty and learn, as well as a good teacher is huge and will save big bucks at mechanics shops or worse, dealers.
What I've also learned is that most non-dealer shops lack the diagnostics to work on electronic engines. That AAA Bus in Phoenix that everyone raves about is the same way. At the time my bus was sputtering and losing power but not throwing a code. The tech was dumbfounded as I tried to explain what I was seeing in the ICP charts in Servicemaxx. He accused me of messing up the ECM with one of those "bluetooth monitors from china" and sent me to the dealer to get the ECM re-flashed which I knew was complete BS. The dealer diagnosed a failing (but not yet totally failed) EGR valve that was causing the sputtering and random issues. I promptly "fixed" myself after I thanked them for the diagnosis with a large check (but not nearly as large as it would've been to have them fix it).
For transmissions, I'll add in be weary of non-Allisons, especially Voith. They're pretty common in transit buses but there's not much aftermarket support for those since they're almost exclusive to government-owned fleets.