Simple first complete jaipur it may take 2-3 days after that jodhpur it take 2 days connectivity is good lot of trains buses are available ...try to stay in hosteller Jaipur
You can explore jaipur in 3-4 days starting from forts which lie at same location. then you can travel to jodhpur via night travel easily and explore jodhpur in 2 days.
Buddy... i can help you with jaipur. if you are going to jaipur , you can visit forts Amber..jaigarh and Nahargarh. You can also visit the local market (bapu bazaar) for shopping and can enjoy Rawat's kachori and also you can visit Ghee walo ka raasta for some good desi ghee preparations. also for dinner you can visit a restaurant named "Thali n more" for authentic rajasthani food. next day you can plan for "chowki dhani" based on Rajasthani village theme. after covering these you can move ahead towards jodhpur.