I'm wishing one our diesel gurus would show up about now , the 2" lift in itself shouldn't normally affect anything to do with the fuel system unless you've inadvertently somehow pinched the fuel line , just looking at your photo that red hose going to the filter is fuel hose isn't it ? And the black hose on the other side appears to be somewhat kinked .
You are using the glow plugs ? The glowplugs are connected and working ? Glowplugs not working or not working properly will make it a bitch to start and could make it a bit lumpy to start with but won't affect the running after that .
I'm almost tempted to get you to spray a bit of start you barstard into the air cleaner to see what happens .