MTDI 2.8 pump issues?

Back story: I have had this 2.8 LT pump on my AHU for four years now. When I originally converted it, I just slapped it on, and timed it to ear. I thought it ran awesome, I put probably 5-6,000 miles on the swap. Then I moved cross country from Nebraska to Utah. It seemed a lot harder to start when it was cold, so I finally decided to check timing. I checked TDC with a dial indicator through the injector hole. I put my dial on, and timing was set at like 2.85mm!!! Way high, so I dialed it back down to 1.4mm. Now it starts a lot easier, but it seems like I'm suddenly getting a lot more smoke from the exhaust, and there seems to be a bit of a stutter or delay when I give it throttle. What should I check next? Compression? Injectors? The injectors are supposedly pp520's, but I haven't checked to confirm. I'm kinda tossing around the idea of going back to electronic and selling off this pump. Any help is appreciated. Thanks.