I have a 98 and a 99 forester l models the 98 isn't looking good underneath because of rust but the 99 looks pretty good and I was wondering how or if I can put the 98 Manual transmission is the 99 that's an automatic?

you can but it's kind of a waste of time.  simpler to sell the 99 and buy an MT. if you have the skills to do that swap, then you can simply sell and buy and be years/miles/$ ahead and it'll take less time. 

swap the trans, driveshaft, shifter assembly, hydrualic clutch hoses/reservoir, pedal cluster, and rear differential. 

and if you want these to work, or match then cruise, instrument cluster, and center console trim.

98 is Phase I DOHC and 99 is Phase II SOHC so the engines aren't interchangeable.  the MT i think should swap but i think speed sensors may have changed, maybe went from cable to electronic.  i dont' think it's a deal breaker but been awhile since i've been into 90's stuff.