Couple of things: Make sure you are not wearing underwear with the padded cycling shorts. Be sure to rinse out the shorts after every ride and rotate their use.
Are you tense on the bike because this is your first road bike? Lower and relax your shoulders. Some people unconsciously shrug their shoulders while riding.
CORE: if it is a weak core you will have issues with fitting but not impossible. But a strong CORE will do wonders in soreness elimination.
Saddle soreness .... again put some miles on your saddle. However be sure the saddle width is for your sit bone width. LBS can measure this and often times swap a saddle out.
You may be too far aggrssive at the beginning of the season. Hopefull the LBS did not cut too much off your steerer tube so that you have play to go up or down with the handle bars. Higher in the beginning of the season and lower as you get accostumed to riding.
Every time their is a change give it some riding numbers and miles. When I get tweaked, I like to go around 2-300 miles before I try something new (unless of course it is causing excruciating pain then sooner) My LBS likes when I come in because I can give him details as to want is occurring and when ( uphill, flats, rollers, descents etc). To this day i still tweak my fit on the new bike yet. A few things are occurring: my core strength is changing for the good I hope; strength training; weight loss. So if I have gained weight from last summer and I have soreness, I usually ride it out til I am at my previous weight and go from there.
Are you curling your toes inside your shoes? Another sign of tensing. You indicated you wanted to go clipless? I am assuming you are using a toe clip pedal then? Are you using tennis shoes to ride? if you are that will affect overall fit as well. Get some shoes that are very stiff so there is hardly any flex to them.
There has been a lot of info. thown your way to digest.
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