Can i put a 99 a4 quattro 5spd engine/engine parts, into my 96 audi a4 2.8?

 

Probably. You'll need the whole wire harness and ECU as well, of course.
Some other things I can think of which you might/probably need as well:
-heater core hoses
-AC lines
-battery wiring
-compare body harnesses because some things probably changed between 96-->99
-intercooler & piping
-front core support, including the frame rail brace
-radiator & hoses
-cat & downpipe, exhaust too
-air box & snorkel, turbo inlet pipe
-cruise control components
-flywheel & clutch
-can use transmission from 2.8 assuming it's a manual transmission

And many others. Basically you need a whole donor 1.8T car.