Cisco,
Like Adam told you, Run it til it breaks.
I have a well-modified 200 in my '60 Ranchero. Headers, Cam, 350 cfm two barrel, valves, DS II, etc. My brother and I have a G-Tech gauge and we did about 50 0-60 runs to test a few modifications.
I put this in front of a 2.77 non-syncro tranny with a column shift. It lasted about a year. To get it to last that long, I drained and flushed the 2.77 and filled it with new clean (You should have seen the crap that came out of it.) gear lube.
I replaced the 2.77 with a T-5. The reason being - it cost almost the same. You'll need an adapter to get the 3.03 to go to the 2.77 bell. They are about the same price as for a T-5 (IF you can find one). The going price around here (ND) is $75 for a 3.03 three-speed and $80.00 for a four cylinder T-5 5-speed. I needed a new clutch, pressure plate and throw out bearing no matter what.
I also kept the 7 1/4 stock rearend with first the 2.77 and now the T-5. After four YEARS and 16,000 of my abusive driving, it now howls loud enough that I don't drive it on the highway without using earplugs (and I still get out of the car saying "Huh? What did you say?" I also bought a four lug 8 inch rear the same week I installed the engine. Insurance.
When I put the 8 inch in this winter, I'll also buy new rear springs. The originals are sagging and allowing a lot of wheel hop power shifting into second gear.
To sum up, I sorry if you were stopped from modifying your engine because of possible drive train upgrades. They are NOT immediately necessay.
Good Luck from 1/2 of the FPH authors