Update:

Took the bike to my LBS today. We spent some time doing measuring, fit, etc. At first he kind of said that maybe I needed to just get used to the bike more. But then after we did some fitting, we found some definite areas for attention.

My seat was perfect in terms of height and position, except one important detail - it wasn't level. Even the LBS owner thought it was level, so we were stunned when we actually put the level on it and it wasn't.

He then checked for reach and believes I need a shorter stem and handlebars a little up. Unfortunately, he didn't have any stems my size and that would work on my bike in stock, so will have to order. His winter hours are Thurs-Sat, so it will be around this time next week. In the meantime, he did swap out one of the spacers that he had above the handlebars to below, so at least they would be up a little.

He did comment that my posture was right on - so that was good to know. All this is new to me.

I also had him make a check of my back tire since I changed it twice - once after the flat and once later to put on Conti GPs. The second time I changed it, I was sloppy and the skewer came out, so I just wanted him to verify it was on right before I ever got it outdoors. He said it was great.

I was also pleased, again, with the service I got from my LBS. It is a very tiny shop (we are a small town) and I really want to support it if I can. I look forward to seeing how everything feels this week with the extra spacer and seat at level, and then reacclimating next week with the new stem.

And thank you all for the great tips. I was putting off going in because I thought maybe I just needed to suck it up and get used to the different geometry. Your thoughts were confirmed by the LBS and while I know I will still need to work on upper body, etc., I'm on the right track. Again, thank you!!!!