The golden rule:  He who holds the gold makes the rules.... Or in this case land.

If you are looking for opinions, stick with it and try to do the best job you can.  I would make it a point to explain to him that doing xyz operation may have zyx consequences. People tend to have short memory and writing things down so they have something to read when you are not around seems to help.  I "convinced" one of my family members I rent from to tile a farm.  I did the estimated payback, voluntarily raised my rent to cover the tile cost (and then some) and managed the project.  After it was all said and done it worked out for both parties. We had talked about it for two years and both of us never did anything until I presented numbers on paper.  It was a clear advantage to making the investment in the land.  Again, write it down and present your case. 

Personally, cutting chemical rates is a recipe for a disaster.  I've seen what half rate chemicals do to a farm around here and it takes MANY years to clean fields back up.  One bad year of weed control leaves a lot more viable weed seeds than one thinks.  A suggestion would be to put together your optimal crop budget and estimated goal.  And then put together another scenario with minimal inputs.   It's pretty easy to find information on the internet about yield loss due to poor weed control.  So you save $8/acre on chem or whatever it is you will be paying for it in this year's crop and more importantly, next year.  It costs a LOT more to clean up a dirty field than it does to maintain a clean field.  Talking from personal experience.

I used to do custom work and got burned because of slow paying or negotiating after the fact.  I feel I do as good as job as any and my time and equipment are valuable.  I stopped custom farming because of the hassle.  Good on you for sticking with it.

One thing that you have figured out is pride probably has a lot to do with it.  "I have always done it that way and it's worked so far" can be a hard thing to overcome.  I am thankful for my family situation that let's me be the operator and make the decisions. I still ask for advice as they have more years but even they will admit the "tools" today are different than they were 25 years ago.

I will go back to the golden rule again.  Your family member does own the farm and you are custom farming it for HIM.  It is his and you have to respect that.  You can still present your case but I would suggest approaching it in a very respectable manner.

Hopefully it all works out for you.