Doors and Windows - Water damage

Ok, heres the problem.

Very bad workmanship on the builders part! (IMHO)

Back door is 3/4" above back deck, no space between house and deck for rain water, no spacing between 1st 3 2x6's so when it rains water has a tendancy to pool on the deck next to the house. first noticed that the kitchen floor was wet after it rained, then door rubbing hard against the bottom door plate, attempted to lower the highth of plate (4 screw to adjust hight) On closer inspection notice that the threshold is bowed up in the middle (obvious water damage). 2nd problem flashing is @ 90 deg so even when the water runs off the deck between the house and decking it pools against house. So now I have two problems!

Do I need to replace the door frame and threshold or just the threshold and can I sawzall the rotted water logged wood out and replace with pressure treated then bend flashing down so water drains off house?

Thanks
Brian

It's more work, but I'd be tempted to pull the whole door w/frame out if you think the subfloor and supporting joists may have enough water damage to need replacement. You could replace the sill at the same time and it would give you more room to work and inspect damage.