I think I can be of some assistance here. I have Thiel CS 3.6's and experienced both of the issues that you described, 1) the harshness and 2) the strange "out of phase" bass quality.
I would first of all say that while I have not listened to the Modright Oppo 105d, my gut tells me that your front end is NOT the cause of the harshness. I would say it is, with very high probability the AMP. I don't know the specific specs for a Conrad Johnson Premier 350 but it sounds like "parkhurst" above identified a mis-match with his CJ amp and the 3.6's. My previous power amp, an NAD 2200pe sounded very harsh and fatiguing with the 3.6's. The layering and detail in my digital recordings was all congealed and compressed in a very fatiguing way. I hated it. o I set out to do something about it. I ended up purchasing a Bryston 4B2 solid state amp. Apparently the 3.6's are present a very difficult low impedence load to the amp. I almost bought one of the hot rodded McCormack amps (used) that I had read quite a bit about. Instead I went with Bryston (new) for their 20 year warranty. The Bryston 4B2 (now replaced by the 4B3 which is even clearer sounding) really has the power that these 3.6's need. My Bryston is also hooked up to a Bryston BIT15 power conditioner which I believes helps as well. With a proper power amp that can handle the lower impedence loads your 3.6's will be much happier.
As to your issue with the bass. First of all see if a proper (solid state or tube) amp that can handle this speaker's low impedence needs helps the bass. Do much auditioning of your music as you make these changes. But my bass had been in focus in my rectangular listening room with the speakers arranged along the long wall. Then my girlfriend re-organized the room while I was at work and decided (on her own) that it made more sense to position the speakers along the short wall. Mistake! I noticed the bass being cancelled out right away. Turns out it was a sonic room node causing some cancelling of the bass energy. We put the speakers back where they originally were and like magic, the bass is back to being tight, and focused again!