the lower hole is the low line and the higher hole is the full line...u want it just below the upper hole...

as for the rpm changes some is normal the engine always runs at higher rpm and a bit richer(wich may be the extra fuel smell) when its cold...i dont know if that level of rpm change is normal forthat motor or not

that clunking in the transmission...my first recommendation would be to have the tranny flushed and a new filter and fluid put in and see if that changes..should do some good for shifting...otherewise u prolly have something internal