1992 honda accord engine trouble?

hey recently i just had someone put in a motor on my 1992 Honda accord ex model and its a manual, now the motor he put in the car came off a automatic one he used most of the old parts from the old engine and only put on a few things like distributor, water belt, clutch and pressure plate, thermostat. Now ever since then when i crank the car and put it in gear it makes some weird sound and when i go to shift the gears it sounds like something is thudding underneath the hood of my car but when i gain some speed it goes away any thoughts much would be appreciated thanks!

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