It doesn't look too much like you're restricting airflow from any of the photos, but I can't really tell. My guess would be the attitude at which your plane sits when on the ground during the takeoff roll. Trailing link gear is great for stability and durability, but you need to make sure the plane always has a nose-high attitude or it will get pushed into the ground and have trouble taking off, especially from grass fields like you seem to have. Most of the issues I've seen with changing out stock landing gear come from this. If I had to guess, that would be the culprit. In terms of weight, I'm guessing your changes are going to be a non-issue. I don't personally have the viper, but from what I've seen, it has excess power when stock, and I've heard of people flying it on 5000 mAh packs, so I doubt you have changed the weight enough to create an issue.
Another thing to try is recalibrating your ESC. I think for most e-flite planes you just plug in the Rx with the throttle on the Tx advanced to full, wait for it to beep, and then drop the throttle until the ESC gives the normal sequence to indicate it's ready. It's easy to accidentally recalibrate an ESC and not notice which can result in losses of performance. The last thing to check is the center-burner installation. Again, I don't know specifics, but most designs I've seen draw from the ESC wires, so it's possible there's some kind of short in there that is robbing you of power.