Howard - who has previously worked at Bolton Wanderers and Newcastle United - will be supported by an additional fitness coach, Duncan Russell, who follows Ince and assistant manager Ray Mathias from his previous employers, MK Dons.
Ince's backroom team is now taking shape after former Manchester United and Scotland coach Archie Knox accepted the post of first-team coach, to be assisted by former MK Dons first-team coach Karl Robinson.
"Mark is someone that has been known to the club and Paul has talked to him and is very happy with him," said Rovers chairman John Williams. "Along with Mark, we've brought in Duncan Russell from MK Dons. It means an extra body in the sports science department."