ok, well then ill just assume that you knew what you were reading and did the alignment correctly. seeing as you are getting 18 watts PEP on SSB, you probably did ok.
if you have the sams manual, look at the voltage readings for all the transistors and ic's involved in your issue. some of these would be the driver and final, TR41 and TR42, and the voltage regulator.
be sure to measure them on RX and TX, as you might have a voltage drop on TX somewhere that could lead you to the bad part.
also be sure that your power supply is adequate. 5 amps constant should be plenty.
if you are getting 18 watts on SSB, then your driver and final are fine, i only mention taking their voltage readings as a way to see if something weird is happening on AM mode.
a guess would be that you are not getting enough voltage to the collectors of the driver and final in AM mode. look for cold solder joints or shorted parts if you have been working in this area.
low power problems can be very hard to determine.
one thing you can try is hooking up an ammeter to the input of the radio.
if the radio draws 2 amps on SSB when modulating it to 18 watts, and also draws 2 amps on AM when you are only modulating it to 5.5 watts, then you know you have a short somewhere in the radio that is drawing your precious current away from the driver and final.
good luck,
LC