90 Ranger 2.9ltr Kicks when floored or low end movement

My ranger has a new clutch, new exhaust system, and "supposedly" had a tune up 6 months ago. This kicking thing has been going on since my first clutch died. I put a new clutch in. After it was put it, we discorvered an exhaust leak in the manifold (r). We replaced the manifold. Skipped less, but still skipped under load (hills, flooring etc). Took to shop. Said I needed new exhaust. Threw in new from the headers back (cat, muff, int, tail). Skipps less and sounds great (minus the worn bearings in my alternator which sound like @%#@%!@$). But the thing still skips and is making me angry. Could I have fouled the ignition by driving it for months with a manifold leak? I am considering doing a tune up including igniction control and distributor/coil. Am I barking up the right tree? Please help, I put in a new tranny, shocks, exhaust, and made this thing look nice, i'd like to keep going. Thank you. There are no warning or check engine lights on, the car appears to think it is running normaly.

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