Frank,
What you are forgetting is the labor charge that's involved in taking the stock pump and modifying it. The only way you will ever get a short shaft pump for cheap is if you know somebody that can do it for you for nothing, or if you do it yourself.
Also, in general, specialty parts places trend a little higher in price than a NAPA, etc... especially when you consider shipping charges and the extra waiting you go through to get the mail order parts. Sometimes where the parts are made will affect the price. Sometimes parts made in Asia can be less reliable than ones made here in the U.S.
Personnally, I am not in favor of modifying wear parts unless it's the only way to make something work. As I have said before, there is more than one way to deal with the water pump issue. It's up to you to figure out what works best for you.
As for buying a press, I have found that Harbor Freight runs sales on there presses fairly regularly. If you are finding yourself taking in driveshafts for U-joints, rearends for bearings, or T5 tranny rebuilds, then you have probably spent more than it would take to buy a good press and do all of it yourself. Just a thought...
