Probably one or the other but that depends on how heavy your tractor is and whether or not your tractor has 4-WD.
Filled tires lower the center-of-gravity of the tractor, therefore help stabilize tractor if you will work on slopes, with or without the Box Blade. R4 tires are always at least six ply. R1 tires are usually four ply. R4 tires have greater punctures resistance, especially sidewall puncture resistance. R4 tires have a slightly greater contact patch with the ground than R1 tires.
R1 tires are better if you have to deal with a protracted mud season.
Adding wheel weight with liquid is much cheaper than adding wheel weight with tire weights. Taking off a liquid filled tire can require at least two people to handle the weight safely.
I have sandy-loam in Florida. I pull a 60" wide, 625 pound Bush Hog (brand) Rollover Box Blade behind my 5,400 pound Kubota L3560 with air-filled R4/industrial tires without losing traction. Your conditions are different. However, I would guess R4/industrial tires would be significantly better than R1 tires for your rock, with the potential to gash the sidewalls.
I do some ag work, although my primary tractor work is in the woods. My land is flat. I hate to compact the soil, which deprives crops of the oxygen they need to flourish. You need enough weight for traction, no more. If you will operate over lawns, you will not want too much weight or you will rut turf.
The most bullet proof transmission is as dependent on operator skill as the mechanics. If your tractor will have multiple operators an hydrostatic/HST transmission is the easiest to use and most proof against inexperienced tractor operators. HST transmissions are only available on tractors up to around 60-horsepower.
HST is excellent for Box Blade use. It produces max torque a low engine rams. That is what you need when commencing a pull with a loaded Box Blade. With HST you forward/reverse just with foot pedal. You do not move a shift lever.
I have operated every type of tractor transmission. Only the simplest clutch and gear requires real skill but I drove only clutch and gear cars until forty years of age, so clutch and gear tractors came naturally. I do NOT recommend a clutch and gear tractor for Box Blade work. OK for field work.
There is no practical difference between MFWD/FWD/4-WD.
I will let a Deere expert address Deere model differences, however weight will be a factor. I learned tractors on Deeres, but that was long ago. My last two new tractor-loader purchases have been Kubotas because the local Kubota dealer is excellent. The Deere dealer is not very interested in <40-horspower tractors.
((You may wish to copy your Deere model questions into the Deere specific forum, which will maximize your replies.))
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