Well I may have a different take
IMHO all of the MOCO offerings have issues and in some cases have good component parts but not a well integrated package. I will explain
There is a lot of passion and bias on the topic because guys plunk down hard earned money to buy these bikes and especially the 110 CVO bikes and then begin the ritual of finishing what the MOCO, HD, has left Half Done
The 06 CVO 103 is not really part of this comparasion. This is comparing a 2011 103 VS a motor change to a SE CVO110 from what I understand, right?
Well the bottom end is the same. Both of them have had issues with cranks slipping taking out oil pumps and camplates, and other parts on the drive side. They just added the SE compensator to the CVO bikes as standard, it should be on all new big twins!
The SE 110 pistons VS the 103 pistons would be a toss up IMO, both good parts on their own. The cylinders also decent parts. The heads on the 103 are decent out of the box and well matched to the motor, and offer the ACR solenoids for easier starting. This 103" is the same motor used in the police bikes (since 2007) and after the addition of the ACR valves has proven very reliable in fleet service. The 110 on the other hand has a very poor service record and the MOCO has replaced more motors with this model than any I can remember since the inception of the twin cam. The 110 has an interesting head but IMHO not that well matched to the motor and the intent of most of the owners. The ports and valves are very large. This is not a bad thing if all out HP is the want but these motors are then saddled with full EPA trim and a very short cam in an attempt to get them to satisfy the government, reliability and what the majority of the owners want for performance. Well they missed the mark there. I talk to these guys every day. They want torque, pulling power for the most part. These 110s run hot as the corrected for cam compression is very high. This heat is really causing most of the issues we see as compared to the 103 which does not run cool but not as extreme. This includes head gasket leaks, exhaust valves seizing, cylinder bores distorting and more issues.
Pass on the 110
See if they will just get the 103" properly tuned SEST or TTS, new pipe less cat and with the proper placement of the new lamda sensors, a cam change, and air filter. It will run well if the dealer knows how to tune and has a dyno. Warrenty will be between you and them.
If you want a motor that will make a differance then just pony up and buy the 120R