Drake,
First of all, you will never draw a unit 41 or 42, or for that matter any good controlled hunt in Idaho as a second choice. There are more applicants than tags in almost all units. Therefore, no second chance tags. You can draw an unlimited tag as a second choice, such as a units 20A, 26 and 27 deer tag. Great rut hunt if you can find the bucks. Tags like this are usually in areas that are extremely hard to hunt and have limited access. Not a hunt for the weekend warrior.
Now back to unit 41 and 42. Unit 42 would be my choice over 41 to hunt for deer. Better deer and more of them. Access is fair in both units, and some ATV areas. Lots of beautiful desert country to look over but few deer. Burns in 42 will put a hurt on that unit for a few more years. They both have the ability to produce a hog, just not many of them. Lots of public ground which is nice. Put in your time and a 170" or better is in the truck. Odds in drawing will be 10% or less in these units.
Best of luck