I'm working on an pedal based on the BTSE-99FX, on the schematic it notes "line level" for input and output.
my understanding is that instrument level is lower than line level, so my questions is can I simply adjust the level with an opamp going in, and again with an op-amp, or simple volume control going out?
yes, you can use either an opamp or JFET amplifier on the input, and the output can just be a resistor divider. take a look at some of the pedal schematics if you want some ideas for amplifier designs. most use non-inverting designs, to get the high input impedance.