You should probably try different settings and/or tubes on the amp. I've had very good results with Les Pauls Customs and stock/low output pick ups in my Mark IV (for high gain / metal). I actually think that these older Mark series amps sound great with lower output pickups PAF style pickups.
I don't remember my settings on top of my head but it's a rather complex amp to set up with a lot of options that have a huge effect on tone. If you just got the amp spend a few more weeks to get used to how each knob and button affects the sound and you'll end up with a great sound. I don't think you need to change the pickups.
Basic idea is to run the first gain stage rather high (7-9), treble high (7-9, adds gain), mid has little effect on sound but usually run it in 5-10 range, bass on 0 (depends on your cab but not more than 2-3, you get the bass from the GEQ). Second gain knob usually a bit lower than first stage maybe 7-8. On the back you can run Harmonics and Triode (triode smoother than pentode). Experiment with the Presence settings, if amp is too harsh pull the knob out and/or run lower settings. Presence knob is quite powerful.
Once you set up the preamp gain and tone + presence turn on the GEQ. Set the bass at desired level (usually have mine a bit above mid point but will really depend on your cab, room guitar etc), general idea is too raise the slidder to just before it gets boomy/flubby. Play with the low mids so that the amp has a good growl but still retains enough clarity. Drop the middle slidder to get a more aggressive tone. High mids and Treble adjust to taste, usually speaking will give slight boost to both of them.
You could also try out some different preamp tubes which could make the preamp gain structure different (some tubes will make it sound smoother, other brighter etc) but at first would really spend time on the amps settings, take a while to get used to.
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