A CREW; MAINT FERRYING AN MD80; EXCEEDED THE FERRY PERMIT'S ALT AND MACH RESTRS.

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MAINT DEFERRED THE AUTO GND SPOILER SYS PRIOR TO DEP. WE REVIEWED THE NONSTANDARD ABORT PROC INCLUDING MANUAL BRAKES AND SPOILERS. DURING TAXI; THE AUTO BRAKE SELECTOR WAS INADVERTENTLY SET TO TKOF POS. WHEN APPLYING TKOF PWR WE HAD A CAUTION AND WARNING SYS WARNING. WE ADVISED TWR WE NEEDED TO TAXI CLR AND DEAL WITH THE PROB. AFTER CONTACTING OUR MAINT; WE DISCOVERED THE BRAKE SELECTOR IN THE WRONG POS. THIS SOLVED THE PROB. (A NOTE IN OUR CHKLISTS ADVISES THE CAPT TO RUN THE THRUST LEVERS PRIOR TO TKOF TO CHK THE TKOF WARNING SYS TO AVOID A WARNING ON THE TKOF ROLL.) THIS WAS OVERLOOKED AND WOULD HAVE PREVENTED THE WARNING ON THE RWY. AFTER RAISING GEAR AFTER TKOF; THE 'R MAIN GEAR UNSAFE' LIGHT ILLUMINATED. WE FOLLOWED SOP; DISCUSSED PROB WITH MAINT; AND RETURNED TO ZZZ1. MAINT DECIDED TO FERRY ACFT DUE TO A PREVIOUS PROB WITH THE GEAR INDICATION. DUE TO THE UNSAFE GEAR INDICATION; THE FERRY PERMIT SPECIFIED A SPD OF MACH .70 AT FL330. AFTER DEP AND RAISING GEAR; ALL UPLOCK INDICATIONS WERE NORMAL. APPROX 1 HR INTO FLT; WE ENCOUNTERED LIGHT TO MODERATE TURB AND AN APCHING LINE OF WX. AFTER DISCUSSING THE FACT THAT WE NO LONGER HAD THE ABNORMAL INDICATION; WE ELECTED TO CLB TO FL370 AT .74 - .75 MACH WHICH PROVIDED A SAFE BUFFET MARGIN. OUR INTENTION WAS TO TOP THE WX AND RESUME THE FLT; PER THE FERRY PERMIT. DISPATCH CONTACTED US AND WE ADVISED OF OUR INTENTIONS. WHEN WE RETURNED TO ZZZ2; DISPATCH ADVISED THAT THEY WERE FILING AN ASAP RPT DUE TO THE FACT THAT WE DID NOT FOLLOW THE RULES OF THE FERRY PERMIT. CONSIDERING THE TURB/TSTMS AND THE FACT THAT THE ABNORMAL CONDITION NO LONGER EXISTED; WE FELT THAT MODIFYING THE FERRY PERMIT WAS APPROPRIATE.