first of all, your ass will soon toughen up and the saddle will become as comfy as a barco lounger. your gluts will offer more support as they tighten up.
saddle height and angle should be looked at by very expirienced racers (who spend long hours in the saddle) and let them assist you in dialing it in.
secondly, a relieved saddle (scalloped away/clearanced in the area of the pubis may be of some help, although i never felt the need to try one.
you should shift your hand position on the bars OFTEN as you ride. this will help to rotate your pelvis on the saddle and keep blood flowing to all areas by shifting your weight distribution and contact on the saddle.
thirdly, i started racing at age 18. i'm about to turn 50 and logged anywhere from 2500 to 8000 miles per season with no affect on the ability to sport wood. dunno what my sperm count is, as i never tried to have kids. i can still wear the wife out, so i think i'm 'ok' in the functionality department.
concern yourself more with conditioning and watching out for all the moron, redneck, asshole drivers out on the pavement!
as far as a new machine goes...
there is NOTHING that compares to the ride of italian steel tubes fitted with campagnolo componentry. test ride a pinarello made from columbus slx tubing and equipped with chorus components.
i noticed your complaint about flats. this is normal and the sign of a rider that is pounding out the miles. in one season, i went thru 36 sew-up tires...and am still proud of that (rather expensive) season.
i would suggest switching to sew-ups for several reasons: faster changes on the road, a more lively ride, more responsive accelleration and more efficiency in the rolling resistance department.
do not obsess about shaving a pound off of the bike's frame or components. obsess about saving rotating mass in your wheels and on your body.
may the wind always be at your back, the sun on your shoulders and your sprint be faster than the dog coming out of the yard to chase you!