New bike, new pains, fit/aero questions

Coming from a road bike background of many years, now I have a new tri bike. I did get a fitting and I can take it back in for adjustments I am sure -- it's just not terribly convenient. Wednesday I did a short ride (20 miles). From that ride I have a couple issues.

Issue #1 Knee strain -- probably saddle height. I did not notice any knee issues during or immediately after the ride right away. A couple days later after a run, though, I am feeling strain in a knee, in the back and maybe center. There was nothing remarkable about my run, it's a distance and pace that I am comfortable with. I'm guessing my saddle is too high for what my knees prefer (definitely higher than my current road bike setup) and that a strain from the ride only became apparent after my run.  I am considering lowering the saddle on the new bike since that's the biggest change that I've experienced recently.  If I drop the seat a quarter to half inch or so, should I also slide the saddle back a touch at the same time?

Item #2 is more related to aero position I think -- triceps fatigued, neck sore/tired. About a half hour into the ride my triceps started to fatigue a little. 45 minutes into the ride my neck was getting a little sore/tired trying to keep my head up and looking forward. I found this thread on another site from a search, and the poster describes how I feel to a "T" (Neck Strain). If I allowed my head to drop forward a little and I look forward by rolling my eyes up and using peripheral vision, my helmet was blocking my view. Now, I guess I can shop for a lighter helmet that's cut a little higher in the front to allow better vision with my head down. Any suggestions on that? Also, one of the replies to the linked thread suggests that this might result from being a little too stretched out. Any thoughts there, or should I just give it a few more rides to see if I acclimate?  Thanks.