Kazekai, I'm running a stripped down version of this and I still get a complete frame freeze every minute or so for 1 second. No idea what's causing it.
I have no idea either. I seem to get that problem when I load certain areas. At first I thought it was the trees but I can be in a heavily forested area and experience no lag so I don't think it's that. It might be something underground since the entire vertical geometry of a chunk is loaded but I wouldn't know because I don't like to mine. (I just steal ore from my friends and leave them pies as thank-yous.)
It could very well be a mod, I wouldn't know which though. I hear negative things about TE's effect on clients but I've been on servers that use it (the city boys I play with can't survive without fancy metal boxes filled with lava) and never experienced lag like this so it might be one mod, but two mods conflicting somehow...
I haven't ruled out this being on my end and am still looking for ways to resolve it but I cannot think of any other explanation for unexplained localized lag spikes