i'm about 6'3"...never encountered QUITE the height differential, but some similar problems. here are a few things i've found...
with missionary, instead of looming over her, keep your torso upright. this is usually most comfortable i've found sitting up on your knees and the balls of your feet while she stays on her back (she may have to lift her hips and butt up a bit for the angles to work, so depending on her flexibility you might want to grab some cushions or something). not sure if there's a specific name for this (reverse doggie? lol), but it's a lot of fun. use her hips and legs to help control and guide and you'll discover all kinds of awesome variations (my ex especially liked when i'd push her feet together and bring them down to about my stomach level).
doggie...check your bed levels. if it's too much trouble kneeling that far down, don't kneel. have her up in the bed while you stand on the floor behind her. if the bed level isn't just right, there are all kinds of tricks to adjust it higher or lower as needed.
shower sex...i don't know what to tell you. one of my favorites, but it's hard enough trying to get the angles to work right when you're closer in height. lol! i've done the pick-the-girl-up thing outside of the shower before (A LOT of fun!), but never in it. probably my lack of a bathmat.
but yeah, generally, just be playful and experiment and find what works for the both of you. that's half the fun right there.