Starting with the last item first, I checked the IRA calculation using only the spouse's income and it matches the allocated IRA.  Glad to know that's the reason and that the IRA deduction wasn't developed by a random number generator.

On the royalty and farm income, I'm entering the royalty income through the O & G screen.  I agree, I've had good success with Lacerte's O & G module.  All my items are set to Oklahoma, and here's what I'm getting:

The Federal amounts on lines 12 and 13 are net figures while the Oklahoma amounts are revenue amounts.  The business income is KS income.  Interestingly, if I create a second Schedule C and set it to Oklahoma and include revenue and expenses of at least $80 each the OK farm and royalty income is corrected.  I'm not sure if the $80 threshold is due to some other field or what.  Also, I just realized that the additional Oklahoma depletion is being deducted.

The OK numbers are small enough the client won't have any tax problems so I can always file a return that is technically incorrect but with a correct result although that's not my preference.  My real concern is with other clients I have who have income in both states and whether they'll be correct.