remote start f 350

Installed remote start /keyless entry system in 2002 f-350 crewcab 7.3L diesel w manual trans w/o factory keyless entry. Unable to start in manual trans mode - 7 flashes, switch to auto trans mode, starts if you hold clutch in. Does the clutch safety switch need to be bypassed? and also noticed when it goes to start, dash lights ,radio,etc. turns on for a few seconds, turns off for a few seconds ,turns on and starts up and runs. h3 connector pin 1 - rd/grn ign, pin 2,5,&8 - yel., pin 3 - gry/yel, pin 4 - grn,pin 6 -rd/blk.

Also, having issues with power door locks, installed on pk/grn and pk/yel wires and didn't work ,looked at wiring diagram and noticed wires grounded at rest position, door lock output is neg switching, so I had to install relays to lock and unlock the doors however, they had to be tied into pk/bk and pk/og  in l/s kick panel between switch and actuators only to have only the l/f door lock operate with keyless entry and all doors operate with door switch.