It's hard to give specific advice without knowing the details of your procedure and your equipment set up. Without reading the attached thread in detail, here are some thoughts...
You seem to be losing a lot of temp in your mashtun. If you are using the keg/mashtun be sure to keep it covered and insulate it as best as possible. The cheap way is to wrap an old coat or quilt around the keg (assuming you are not using direct-flame). The more expensive way is to buy some flexible insulation. If you want to continue to use a cooler, you may want to invest in one that is not damaged.
Be sure that you are getting a good crush on your grains. One of the most common reasons for low efficiency is a poor crush. If you are having your grains crushed by a supplier, keep in mind that they may not have their mill set correctly and that the crush can vary from batch to batch and from one supplier to another. If you do a search on the NB forum, you can dig up pictures of properly crushed grains for reference.
What is your water/grain ratio? If your mash is too thick, you can get a lot of temperature variations and uneven enzyme activity. The mash should be thin enough that you can get a good, even mix with no doughballs. Wait at least 5 minutes after dough-in to be sure that your temperature has stabilized before monitoring.
When calculating out strike water temperatures be sure to factor in the starting temperature of your grain. For instance, if your strike water temperature is not high enough for the starting temperature of your grain, you will see a pretty significant decrease in temperature until it stabilizes. This drop in temperature can be confused with a temperature loss due to your system.
Be sure to compensate for water absroption loss when you determine your strike and sparge water calculations. The sparge water volume becomes less of a problem if you fly sparge since you can just overadd water to your HLT and keep sparging until you hit your target pre-boil volume.
You can try to fly sparging with your set up to see if you get a better efficiency than with batch sparging. I personally fly sparge...Not that I think that it is better, it is just what I have always done. When I have batch sparged with my system, I did not get a very good efficiency (50% vs. a typical 80%).
Keep in mind that it is very important to define your system when brewing all grain. What I mean by define is that you need to know things like dead space volumes, volume loss to transfers and boil-off rates as well as being able to accurately measure volumes pre- and post-boil in your kettle. Knowing the details will make it much easier to trouble shoot and adjust your recipes as needed.
As for software, I have to say that I highly recommend software for serious AG brewing. It is by no means a necessity, but the ~$23 investment will pay for itself through more accurate recipe formulations (i.e. less waste of materials), time savings and peace of mind. Beersmith and Promash are the most popular and both are good. I have been using Promash for about a year and I absolutely love it. All your necessary calculations and conversions (including temperature corrections for your hydrometer) are in one package. All the specifics for the most common grains and hops are also built in to the sofware. Once you define your brew system, you can set the defaults (i.e. boil off volumes, extraction efficiency, etc.) to YOUR system. It makes formulating recipes a breeze and it is nice to instantly see the affect of varying ingredients (hops, grains or sugars) without having to redo long-hand calculations.
Good luck.
