gearbox

HI, I RECENTLY PUT A 16V KR ENGINE AND GEARBOX INTO MY MK 1 CABBY AND NOW I CAN ONLY GET IT INTO  1,2,3 GEARS, NOT 4 AND 5 , CAN ANY ONE HELP ?

Have a look at the Linkages. Other than that Gunna need more info.

the car came with a 1.8 kr engine with the same gearbox and it went into the gears fine, then i took the engine and gearbox out and then bought a new engine which is a 1.8kr the same as what it came with and put the gear box back on and now it only goes into 1,2,3, not 4 ,5 it makes a knocking sound as i change gear.

As above......look at the linkages, and adjust as needs be.