1998 Honda Civic LX looses power while I drive

I have a 1998 Honda Civic LX that was converted from automatic to 5 speed. It hesitates while I drive, only sometimes. Normally it does it when I am pulling off from a stopped position or when turning the corner and then accelerating. I will have my foot on the gas, but it won’t gain speed unless I hold in the clutch and rev up the engine then it will pick up speed and go fine. Then sometimes it also hiccups while driving without accelerating, I can feel the car jerk a few times and start to loose power. I will need to down shift to third, or most often 2nd gear and rev it again to gain power and to pick back up speed. Things done to it since i bought it only a few months ago by the person (who is a mechanic) I bought it from: oil change, fuel filter changed, Lucas gas treatment added (by me), new exhaust system installed, starter replaced. I am nervous that it may be rear-ended, or t-boned in heavy traffic. Should i have the fuel filter checked? is that expensive? HELP

I would have the fuel pressure checked. Fuel pumps can be intermittent.

When the transmission was swapped, was the ECM also swapped?

I don’t know if this applies to a '98 Civic, but some makes and models utilize a different ECM for auto trans models and manual trans models. If you have the wrong ECM, it is possible that this is causing drivability problems.

+1 to VDC’s post.