I am new to savage 99s but recently learned a valuable lesson with one. The rifle was exhibiting difficult loading of the 3rd and more rounds in the magazine. Also, unbeknownst to me (this is my first 99), the lever didn't positively "click" closed, I just had to squeeze it really hard to be sure it went fully into battery. This was evidence of a problem that I was unaware of and should have fixed earlier, so I post this to help others in this situation.
Long story short, the culprit was the magazine screw getting loose. If you want a visual go to numrichs for the parts diagram so the following makes sense.
When the magazine screw gets loose it extends into the action and blocks a part that makes it hard to close the lever/bolt so you have to "squeeze" it closed right at the end of the lever travel.
To see if you have this problem take off your front handguard and observe the front screw on the magazine cylinder. If you can turn the nut on it with a regular flat head screwdriver without risking stripping it is probably not tight enough (correct me if I'm wrong savage owners, this was true in my rifle). What you need to do is take a large flathead screwdriver and file a square notch of the correct size in it (takes 2 min in a vise) so that you can tighten this nut further than possible with a regular screwdriver. You need a gap in the flathead for the screw to fit through while turning the bolt. Once you have done this you can tighten the magazine screw correctly and the lever should work much more nicely for you.
I tried 3 or 4 times doing this without the modified screwdriver and it just didn't work, I was blaming all sorts of other areas of the action when I just needed to tighten this a turn or two beyond what you get with a regular flathead, so please try this before doing more complicated things.
While you're at it you can adjust magazine tension if needed but read up on that elsewhere as it is beyond my knowledge level. I did it by trial and error but there is a pin and springs so read about it from someone more knowledgeable than me so you do it right.
Hope this is useful to someone,
Andy