The 4% is as a comparison to what is considered Energy Star for a window at the time (U-0.30).
When you re-run the numbers for a decent triple pane window (U-0.18), saving jump up a decent bit. Certainly won't pay for itself in a couple of years, but if you are quoted a reasonable number, it may not be a bad investment.
Running that calculation with your math and the better window = $300 in savings but you are show a huge amount of glass there at 1,000 sq/ft.

U values alone (conductance) are only part of the energy loss/gain from windows. Air infiltration, especially in older windows may be a much larger contributor to energy loss a gain. From Wikipedia - " In typical modern U.S. residences, about one-third of the HVAC energy consumption is due to infiltration. Another third is to ground-contact, and the remainder is to heat losses and gains through windows, walls, and other thermal loads. As such, reducing infiltration can yield significant energy savings, with rapid payback. In cold climates, with a 15 MPH wind, residences often have air exchange rates of 1.0 to 1.5 ACHs, far in excess of the ventilation air needs and are thus called loose construction. It is very easy to reduce infiltration rates to less than 1.0 ACH. Smoke candles and blower-door tests can help identify less-than-obvious leaks. The Weatherization article describes methods for energy savings further. If infiltration is reduced below 0.35 ACH, it is recommended that mechanical ventilation (typically an exhaust fan or heat recovery ventilation) be implemented. Wikipedia link on infiltration

If you are interested in other resources in evaluating window performance and human comfort then the rest of this might be of interest; sorry it is such a long post.

Thank you both, as I find it of interest and value to understand and then seek input from trusted professionals about window choice. @Windows on Washington I used 1,000SF in my calc just to make it easier for anyone else to do mental math to do an approximation say if they had 600SF of windows.

@Ikbum_gw thanks for info. It was actually my quoted comment from Windows on Washington in an old thread on Air Infiltration performance that got me researching window performance stats and how absurd it is that AI stats are not required to be easily available to consumers. I agree that the minimum requirement of <0.3 CFM seems like way too much air leakage, and is perhaps a much bigger difference comparing window X and Y than other performance stats.

In case it is of value to any one else delving into this area and evaluating their window options, I found this Lawrence Berkley Lab research study https://www.energystar.gov/sites/default/files/WindowsEnergySavingsAnalysis-LBNL.pdf on window performance/efficiency very helpful. For Northern climate zone and based on their assumed typical home (which might not closely match your own so YMMV) they found that annual energy costs were the same for a window rated at U 0.27 SHGC 0.27 AND one rated at U 0.28 SHGC 0.32

So the rule of thumb they suggest is 0.01U = 0.05 SHGC
Personally I find this very helpful in comparing windows as often window X might be a bit better in U value but not what I think I want for SHGC.

Here is a part of that article summary and my highlighting two windows with same annual projected energy costs as an example:

And going farther if you really want some helpful and fascinating reading on window comfort is this 91 page study in a test lab attempting to understand human perceived comfort when a window is much colder (winter type condition) or much warmer (summer) than the air in the room. http://www.cbe.berkeley.edu/research/pdf_files/SR_NFRC2006_FinalReport.pdf
An important take away for me personally is that people are less tolerant being next to a warm window than being next to a cold window. I will have a key sitting area within 3' of a window so the research is highly relevant to me, but perhaps many others.

The SHGC is an important observation but most applicable if the home is set up to take advantage of passive solar heating. I am more sensitive to cold so I guess there is a personal aspect to this but all good data. Thanks.

http://escholarship.org/uc/item/5p95w76m#page-1http://escholarship.org/uc/item/5p95w76m#page-1

@Windows on Washington Thanks for link to article. It is nice to see a simulation study done by city and indicating Heating degree days, and while this is still "average" home result, it does give more food for thought than the simulations I had seen which simply used the much larger sample area of North climate zone which has tons of variation within it. Of course these studies make the easiest assumption that all the windows are divided by four and appear equally at each compass orientation AND that nothing is done differently re: overhangs. While track homes might be built that way, it is probably totally off for the "typical" person on this forum so it is tough to extrapolate from these studies to ones own situation.

And yes many people are report greater personal discomfort being next to a too cold window or wall than one that is too warm, but in some situations mitigate the former (seasonally) with portable baseboard heater is easier option than mitigating a too warm window. I think both need to be planned for in many northern climate zones and personal (dis)comfort sensitivities are an important element.

I am realize that I often take for granted windows (doors) that work well but that for some rooms within a house careful planning can have great pay off. With the options of tweaking glazing coatings now things can really be dialed in pretty well.