A couple of things come to mind in regards to your question. I will do my best to address each one.
1. Air handler / HVAC located in an unconditioned space. This would not be the best choice/ location on efficiency. However it would be best to make sure all the ducts and the equipment in this area are 100% sealed with duct mastic-sealant and properly maintained by a licensed A/C contractor in your area.
2. Cathedral attic space area is a huge problem in my opinion in regards to your description above. Based on DOE zone (3) for proper insulation it would be best if your R-value in the attic (cathedral area) equaled R-38 (cathedral best). You do not have enough insulation and if not done correctly you will continue to have issues every electric or gas bill!
3. Regarding R-11 insulation X2 with Kraft paper on both sides, from your description its sounds like you have several types or different R-value in the attic. Please consider the R-value must have a weighted average of R-38 for cathedral ceiling and R-38 to R-60 for general ATTIC space, no gaps, consistent density, and level continuous coverage. Without seeing pictures I would highly recommend you have a local insulation contractor check your home and review what is going on with the R-value up close---such as type of insulation, was it installed correctly, attic convection (retaining heat), heat transfer, thermal bridging, and solar heat gains.
4. No mention of a fireplace. This area will have to be checked for leaks and how it was insulated if you have one. We find many issues in this area on older homes and potential fire hazards if the wrong insulation was applied near a combustible source.
Great job sealing the holes with great-stuff; we call this the low hanging fruit and yes it will help. However if you truly want to see a difference in your energy and fuel consumption, the attic insulation will have to be installed correctly to R-38 to R-60 and the duct-work 100% sealed.
In addition to an unconditioned attic I have seen some homeowners add what is called a "solar attic fan" to help with venting the attic, however I'm not sold on the idea!
I believe in proper insulation (building science sealing the envelope) and proper ridge or gable vents with enough soffit vents installed. Remember the solar attic fan does not work when the sun goes down and electric attic fans could cause the home to go negative plus cause more of an issue if not size or installed properly.
FYI: I work for a local power company. I would recommend you contact your local power company to see if they offer any assistance or a free home energy audit or survey. They would be the best choice in my option because they will not come across as trying to sell you something. They will make recommendations based on facts and true energy saving measures that have proven to be effective in your area. Please contact them before you spend any more of your time or cash.
Successful energy reduction, upgrades and maintenance involves a more efficient use of energy through controls and enhancements. The enhancements usually require an initial investment that will offer a yield in financial savings from reduced energy costs.