I bought my first road bike off (raleigh clubman) a guy a few months ago and I really am not sure what was going on but the bike was out of sorts for myself. I am pretty mechanically inclined so I have taken a very patient process to fitting the bike to me and have been pouring over these forums and many other articles for quite a while. In summary:

-Seat was low and saddle was at a positive angle to level.
-Steam was at a positive 10 degree angle on top of all four spacers (mind you this guy was shorter than me, I guess he was going for a more upright fit.
-handle bars were rotated in the positive direction
-hoods were high up the handle bar so that bottom of the brake levers were 45 degrees away from pointing in the direction of travel.

So what I have done was restore bars to level, hoods moved so brake levers were at about 90 degrees, raised stem and lowered seat. Then I sat on the bike and tried to gauge a few things. I rode around and had some pain in the front of the knee so I raised my saddle and angled it in the negative to reduce some family jewel pain I had. Long story short I didn't know about the seat fore/aft adjustment with regards to my pedals and I didn't know the stem was upside down. This past weekend I adjusted the fore/aft adjustment, tried to do the test where i place my heel on the pedal and straighten my leg to find seat height and I flipped the stem. I went on a long ride and had achilles pain in both feet after the ride and mild hand numbness at mile 35 out of 40 total which was a huge improvement so I know I am on the right track with the handle bars. As it turns out, regarding my achilles, I had the seat slightly too far forward and after my adjustments tonight: about 1-2 inches too high. When I did the heel test I made sure to get warmed up and focus on keeping my hips stable (I think I cheated last time), and made sure that I could apply power throughout the stroke with my heel instead of power for about 170 degrees and then sort of floating with moderate pressure for the last 10 degrees. So my main question is now that I have done these adjustments my saddle looks a little low compared to what I am used to ( I'd say I have 4-6" exposed but it just looks funny to me...) but the cranks are long (175mm) so I assume the relationship between my longer crank arms means the seat will have to lower a bit to get the proper leg extensions. Is this a correct assumption? I also dropped the bar 2 spacers after making these adjustments and rotated it close to level if not a bit negative to get my wrist angles better. I am excited to try this set up but I just wanted to see what you guys thought.