With the 361, it'll be easier to over-cam it due to its smaller size. The stock cams were quite tame, by modern standards. The heads on the 400s, being updated 906s, have been proven to flow the same as the 906s, after a small bit of porting (as in the Mopar Perf porting templates' use). Looking at the distributor specs (initial base timing and the mechanical advance totals), total timing was still past 35 degrees btdc, which is just shy of the allegedly optimum 38 degrees btdc, even with the 7.5 degrees btdc base timing on the '72 400 2bbls.
To me, the main issue with the cylinder heads would be if they were 4-bolt or 6-bolt hold-downs. Which would mean that matching valve covers would be needed. Don't recall when that change was made in the earlier '60s, though.
The smaller cylinder bores of the 413s and 361s could mean that the "smaller than 2.08" intake valves are possibly on the 361s. Still sized proportionately to the engine size, though. The larger valves could become shrouded easier by the larger valves, which could negatively affect ultimate port flow. But using "under-cut stem" valves might be a good option, past basic port clean-up on the heads.
Many people perceived the 400s to be "dogs", when the specs were somewhat the opposite--except for the 1.0+ lower compression ratio. Cam specs had a slight bit more lift and duration, with the duration being there for a little bit more residual EGR in the cylinders at lower rpms, but would also help power on the top end. Ford did that trick on their '74 351-C HO motors, too. Carbs were a bit leaner on the lower rpm areas, too, but the cruise mixture should have still been 14.7 a/f ratio as it had been for decades prior. Base timing was a bit lower, but that's easy to change in order to get to the 38 degrees level (either with a bit more initial lead and/or with the Mopar Peft advance curve kit.
The OTHER observed issue with the pre-66 B/RB motors was the very restrictive factory log exhaust manifolds! With an outlet hole of 2.0" at best. So an upgrade there would be good to do, with ANY of the earlier B/RB engines. Then following that with a good under-car exhaust system of at least 2.25" mufflers and pipe.
Any rebuild will probably need .030+ pistons and new rings, by observation, in order to get to "fresh metal" in the cylinder bores. So any of them would need new pistons, as a general rule. It might also be that any cast pistons will not be the factory 10.0 cr piston equivalents, possibly more like the 9.2 cr 2bbl pistons (piston crown height would be the key thing to look at). But the 400s would be an issue as they only came with 8.2 cr, which can be compensated for by milling the later heads to the 73.5 cc specs of the earlier castings (which then makes them look suspiciously like small block Chevy heads, especially if angle-milled). Using thinner head gaskets is another trick to boost the 400s resultant compression ratio. Using forged pistons, "close fit" if possible, can possibly be an easier route to higher compression, but with more expense than the cast pistons. Other than the lower compression ratio, the Data Book for the 400 HO showed it to still have the "guts of a Road Runner" with a lower compression ratio Upgraded material bearings, "more" cam, double-roller timing chain, etc. FWIW
The 361 might be an interesting build with something like the Chry 256/260 cam, cleaned-up power cylinder heads, later model exhaust manifolds (or headers) with the bigger pipe exhaust system, something like the MP electronic ignition kit, a 650cfm carb and later model intake manifold. In other words, basically what you'd do with a 383 but with one-notch lower on the cam specs.
Several possibilities to consider. Thank Davea for pointing out the issues with the earlier TF mounting issues.
Just some thoughts,
CBODY67