I've just fitted myself to my new (to me) road bike and my tip would be to work on the fit, step by step.
(i) Saddle Height - make sure it is level first! Using a spirit level!
(ii) Cleats - Not sure if you are using shoes with cleats but get these to a neutral position at least then work to get them in your ideal position across the ball of your foot and angled to suit your natural toe-in / toe-out
(iii) Saddle Front/Rear adjustment - I was given this advice by a friend: -Rough rule of thumb on saddle positioning with a "traditional" roadbike
If you're sat on the saddle, with your hands on "the hoods", if you look down, the spindle of the front wheel should be obscured by the handlebar. If you move your grip to the "tops" of the bars - i.e. the straight bit near the stem, then the hub should be visible behind the bars (i.e. between the bars and the Bottom Bracket) and if you lean forward onto the "drops (i.e. with your hands around the curved bit of the bars under the brake levers) then the hub spindle should be visible in front of your handlebars (i.e. forward of the bars, toward the front of the bike) That's the "quick and dirty way" to set up the saddle fore-aft.
The better way needs someone to help you, and a few tools.
The traditional method for achieving horizontal saddle position is to position the rider's saddle so that the bump below the knee (the tibial tuberosity) is over the pedal spindle with the crank horizontal to the ground. Get on the saddle and clip in, then get your assistant to drop a plumb line from just below the kneecap towards the pedal - slide the saddle fore or aft to get the line to drop through the centre line of the pedal. If you move the saddle far back or forward, you may need to tweak the saddle height too - further back gives effectively a slightly higher saddle, further forward effectively slightly lower. Its an iterative process, and may take a couple of tries to get it.
At that point, you then repeat the "where are my bars in relation to the hub" exercise, and hopefully (if you're a "normal" shaped human being, and the bike has the correct length of stem fitted) you'll find its pretty near spot on. If it's not, you may need to get a longer or shorter stem.
Hope this helps