I have a 5 speed and a toytec 1 inch body lift also. I do have a Hurst short throw shift though. Body lift shouldn't effect the shifting per say. The shift boot should have enough give. It could be coincidental, the symptoms you describe sounds could be syncro wear, providing clutch action is alright. Can try changing the gear lube with a fresh batch. Also the clutch cylinder and slave cylinder could be failing, but I swapped both mine and no change when I had your same symptoms.
2nd gear hard shift is a common syncro symptom, had one myself on another transmission. It also would pop out of gear from a dead stop if I did lazy quick shift into 1st, I'm thinking the gears were worn also. I just threw out the old 5speed and found a good one cheap and rebuilt it.
If the symptoms get progressively worse, time for a rebuild or swap out if you can find a good one.