* Bellhousing: The 250 straight-six and the 350 small-block use different bellhousings. You'll need a bellhousing specifically for a 350 small-block mated to your 3-speed manual transmission. Finding the correct bellhousing might be challenging, depending on the specific transmission you have (there were variations even within the 3-speeds).
* Clutch: The clutch itself might also need to be changed. Even if the diameter is similar, the pressure plate and flywheel will be different for the 350. You'll likely need a clutch assembly designed for the 350 and the specific 3-speed transmission.
* Other Potential Issues: You'll also need to consider the engine mounts. The 350 will likely require different engine mounts than the 250. Exhaust system modifications will almost certainly be needed. Possibly the driveshaft length, depending on the engine and transmission combination. And finally, proper engine wiring harness will also be critical.
In short: It's doable, but it's not a simple bolt-in swap. It requires significant mechanical knowledge, specialized parts, and potentially some fabrication. Expect to spend considerable time and money on the conversion.