I'd get a $25 code checker, and start there (even available at Walmart). Have you changed the fuel filter lately? (I make it a yearly thing). Is your fuel pump whinning?
Have you replaced the stock clutch cable? The stock rubber grommet in the firewall could be worn out... allowing the cable to flex, and the clutch to dis-engage... this slippage can cause some bucking (but it doesn't really sound like this).
The EGR only operates while cruising (not at idle or WOT)... shouldn't be a problem.
The EGO sensors adjust the fuel accordingly (when in closed loop). At WOT, the computer only relies on the MAF reading, and uses the stock calibration table (programed in the computer). If the MAF isn't functioning properly, this could be a problem.
Also, when you use a calibrated MAF to fool the computer, you get a little extra timing advance... so make sure your base timing isn't too high... maybe try it back at 10BTDC.
At WOT, you start pulling more vacuum, so the fuel pressure will actually drop (it doesn't need as much pressure to inject the same volume into the low pressure cylinder/intake).
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