2008 Toyota HiAce manual gearbox only selects third and fourth gear

There’s a very good chance that your problem concerns the cable or linkage that connects the gearstick in the cabin with the actual gearbox. It’s very common for one cable or linkage to operate half the gears, and a second linkage to operate the rest. If this linkage has fallen off or become detached somehow, there’s no longer a physical link between the gearstick and the transmission selectors for those gears. At which point, it’s impossible to select the affected gears.

A quick check under the gearbox will confirm whether this is the case, and fixing it should also be a simple case of reattaching the linkage or possibly replacing a broken cable.