Longer cables shouldn't make a whole lot of difference unless your talking 15-20ft. longer.
As long as they're connected right a couple of feet too long won't hurt, a couple feet too short? That can affect the shift, throttle.
If you just changed the powerhead, then experience hard shifting then the problems in the lower unit or the linkage.
When shifting without the motor running you will need to turn the prop or the linkage will bind even possibly break something, VERY important you do this.
Setting up the shift and throttle cables: SHIFT: unhook the connectors(both shift and throttle) at the motor(make sure the linkage is free)spin prop and shift between the gears a couple of times then end in N then the cable end adjust it so it just slides over the connector. That should work ok
The THROTTLE: spinning the prop and move through the gears again ending in N Then adjust the connector so it's close to the stud and needs a bit of pressure to make it slide over the stud.
Hope this helps.
REMEMBER to spin the prop as you do this if you want good results.
IF?? you don't have a helper, you can use a jump box to make the motor turn. Just pull the safety lanyard off so the motor doesn't start.