I have just started routinely riding the TT bike (Trek equinox 11) as I get ready for the season. I find that my quads burn a lot more than I’m used to compared to my road bike while in the aerobars. Power numbers are lower too, but I am tired today after yesterdays big day run+lift+ride.
I’m thinking that I need to raise my stem a bit to open up my hips. Does anyone out there have other ideas?
Not without seeing pics or knowing more details. I routinely train about 60% road bike and 40% TT bike. If I go for a long stretch without touching the TT bike, I feel some soreness here and there. The positions are different, so muscle adaptation is different and takes a little time. That may be all that’s going on with you. But without more info, we can’t judge if your position is any good or not. Post one (if you dare) and we’ll be glad to judge you … I mean, give you some feedback! 
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Same here. Just go back on my Tri bike a week or so ago after riding my steep seat angle road bike all winter. I Feel noticeably weaker and am quite a bit sore after my normal rides. In addition the position my tri-bike was in at the end of the fall is far too to aggressive for me right now. To try to bridge the gap so to speak and transition back into TRI position with less shock to the system I raised my bars a spacer and kicked my seat back a degree or so on the rails. I hope In a month or so I will be back in my regular form on my TRI bike. This was a bit frustrating… considering the hard work I put in all winter…The first week back on my tri bike felt like I had taken the entire winter off from riding.