There are differences between the two of course. First, I run Millennium so that is where I come from. And, I am an enthusiast and not an expert or a wrench. I did build my engine top to bottom with machine work done by KT Cycles since I could not do that work. So asking me a lot of questions is probably useless since I have probably written below everything I know.
I have not seen any heads up comparisions in terms of power and in terms of longevity. I think the differences are insignificant. Nevertheless, those insignificant differences led me to choose millennium because (right or wrong):
1. I thought aluminium cylinders as opposed to liners would disperse heat quicker and better. I live in Texas and it gets hot. I have a big Millennium build and it gets hot quickly, nearly as soon as I start the engine.
2. Nikasil is good enough for Continental air cooled aircraft engines, Ferrari, BMW, Jaguar etc. so it is good enough for me.
3. Piston selection is a bit different between the two: soft forgings v. silicon forgings in the Axtel system (I seem to recollect). Not too sure that Axtel doesn't have an edge on that one, but unsure. I know I would not use KB's hypers since they are too hard IMO. But then again the hypers may work with Nikasil better than they do with sleeved cylinders. But the hypers are RPM limited more so than forgings which might be a factor for "A" motors.
4. Balance factor: all the way up to and including the 114 Millenium you can install that kit and substitute tool steel wrist pins for the kit supplied wrist pins (which are lighter, the tool steel ones) and be within acceptable balance tolerances (under 7 grams per piston over stock weight). I do not know if that is true with the Axtel kit. Maybe someone will chime in. If it is not true with the Axtel then that should be a very significant factor to me. Of course, you could spring for the SnS engine which supposedly comes balanced, rotating and reciprocating parts. But, I wanted to build mine and not put in a crate engine.
5. I thought the Nikasil cylinders were trick. That may sound funny, but it was a factor for me and is better than buying a piece of chrome because it looks good, IMO.
6. Warranty was a factor. FWIW, I bought the kit from SBC and then traded that 98 kit (unused and still original boxing) to Brian Nallin for a little bit larger kit. ;-)
Finally, a friend around the corner built the 107 axtell with the BCG dual FI system and runs Wood cams. I built a larger engine and run the Kuryakyn TB with Red Shift cams. Both bikes run as expected. Both are still running well. And the only differences have been I had significant tuning issues with my DTT WEGO II and he did not with his DTT WEGO II because he used the BCG dual FI TB.
Oh, BTW, neither engine is stroked all the way up to 114 ci and you will use the stock 88 crank and not the 103 crank since you get the cubes with bore, 4.25", and not the stroke which is 4" on the 88.
Hope this makes sense.
Seabrook Trick Bagger