No real problem with mashing a bit longer, try it and see if it helps.
As for your other options, I'd wind it back a bit and start at the real basics, bit of a check list: -
Is the milling consistent and effective, I've seen some shocking crushes from both home brew shops and home brewers.
Temperature really is king, have you got a good quality glass laboratory thermometer to use as a reference? These aren't expensive (~$20).
pH really shouldn't be all that big an issue, if you ask around your local brewing community and take a long hard look at your local water supply, you should have a fair idea what to add salts wise, if in doubt add 100ppm of Ca in an appropriate form (to taste), maybe a little acid (I use Lactic) or acidulated malt
This one might surprise a few people, if you want high efficiency look at your sparge. In a modern brewhouse sparging can take from 90 to 240 minutes, that's in a really well designed high speed lauter, a lot of home brewers think 30 minutes is being really patient.
Mash thickness is interesting, thick mashes favour the activity of the enzymes that break up Protein and other structural parts like Glucan, thinner mashes favour Amylase activity, so a thick mash is good for high adjunct, less well modified malt and for beers with a pronounced malty bias (think big Pommy beers) thinner mashes are better for lighter more delicate beers like Lagers.
This ties in with L:G, the more water you mash in with the lower the OG of the first runnings will be. The less is left in the grist to extract during sparging. There is an equation that describes this pretty exactly
oP of first runnings = CGAI/L:G+CGAI
oP Plato, the alternate way to measure SG is %WW sugar in solution
CGAI is the potential of your malt in the form of Coarse Grind As Is (so the malt you are using including its moisture)
To get from oP to SG=(4*oP)/1000+1 is a pretty fair approximation (good to 1.0001)
If we assume that the CGAI is about 75% (0.75in equations) which is pretty typical for a modern good quality base malt and it takes at least a L:G of at least 2:1 to cover the malt in water - well easier in excel
If you want to get creative you can work out your efficiency, the mass of extract left in the malt, even the best amount of sparge water to strike water, how long to boil (given a known boil off rate) and a bunch of other bits and bobs.
At a small (home brewing) scale it probably isn't worth getting too excited, just use a bit more malt, don't over sparge and follow a sensible mash regime.
Mark