SendMessage and SendWait will always have those sorts of issues (especially app-to-app), e.g. the user clicks someone on the screen at exactly the right/wrong time. Really the only way I know to reliably do this is by hooking onto the mouse/keyboard and take total control... its hard and painful.
Note: there are plenty of professional macro'ing software packages on the market (faking keyboard input, mouse movement, clicks etc). Some are very sophisticated with their own programming language and will possibly do what you want. Google "windows macroing software" and you will find heaps - I recommend you do you research, trial several packages til you find one you want and then purchase it.