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Rod Length

The long at short of it: Short Rod is slower at BDC range and faster at TDC range,
Rod/Stroke Ratio -- 1.60  -- 1.80

Long Rod is faster at BDC range and slower at TDC range.
Rod/Stroke Ratio -- 1.80  -- 2.0
Long Rod:

A. Intake Stroke -- will draw harder on cyl head from 90-o ATDC to BDC.
B. Compression Stroke -- Piston travels from BDC to 90-o BTDC faster than short rod. Goes slower from 90-o BTDC to TDC--may change ign timing requirement versus short rod as piston spends more time at top. However; if flame travel were too fast, detonation could occur. Is it possible the long rod could have more cyl pressure at ie. 30-o ATDC but less crankpin force at 70-o ATDC. Does a long rod produce more efficient combustion at high RPM--measure CO, CO2? Find out!!
C. Power Stroke -- Piston is further down in bore for any given rod/crank pin angle and thus, at any crank angle from 20 to 75 ATDC less force is exerted on the crank pin than a shorter rod. However, the piston will be higher in the bore for any given crank angle from 90-o BTDC to 90-o ATDC and thus cylinder pressure could be higher.
D. Exhaust Stroke -- Long rod will spend less time from 90-o ATDC to BDC--allows less time for exhaust to escape on power stroke and will force more exhaust out from BDC to 90-o BTDC. Could have more pumping loss! Could be if exhaust port is poor, a long rod will help peak power.
 
Short Rod:

A. Intake Stroke -- Short rod spends less time near TDC and will suck harder on the cyl head from 10-o ATDC to 90-o ATDC the early part of the stroke, but will not suck as hard from 90-o to BDC as a long rod. Will require a better cyl head than long rod to produce same peak HP. Short rod may work better for a IR or Tuned runner system that would probably have more inertia cyl filling than a short runner system as piston passes BDC. Will require stronger wrist pins, piston pin bosses, and connecting rods than a long rod.
B. Compression Stroke -- Piston moves slower from BDC to 90-o BTDC; faster from 90-o BTDC to TDC than long rod. Thus, with same ign timing short rod will create less cyl compression for any given crank angle from 90-o BTDC to 90-o ATDC except at TDC. As piston comes down, it will have moved further; thus, from a "time" standpoint, the short rod may be less prone to detonation and may permit higher comp ratios. Short rod spends more time at the bottom which may reduce intake charge being pumped back out intake tract as valve closes--ie. may permit longer intake lobe and/or later intake closing than a long rod.
C. Power Stroke -- Short rod exerts more force to the crank pin at any crank angle that counts ie.--20-o ATDC to 70-o ATDC. Also side loads cyl walls more than long rod. Will probably be more critical of piston design and cyl wall rigidity.
D. Exhaust Stroke -- Stroke starts anywhere from 80-o to 110-o BBDC in race engines due to exhaust valve opening. Permits earlier exhaust opening due to cyl pressure/force being delivered to crank pin sooner with short rod. Requires a better exhaust port as it will not pump like a long rod. Short rod has less pumping loss ABDC up to 90-o BTDC and has more pumping loss from 90-o BTDC as it approaches TDC, and may cause more reversion.
 
Notes:

1. Short Rod in Power Stroke -- Piston is higher in the bore when Rod-Crank angle is at 90-o even though at any given crank angle the piston is further down. Thus, at any given "time" on the power stroke between a rod to crank pin angle of 10o and ie. 90-o, the short rod will generate a greater force on the crank pin which will be in the 70-o to 75-o ATDC range for most engines we are concerned with.

2. Stroke -- Trend of OEM engine mfgs to go to longer stroke and/or less over square (bore numerically higher than stroke) may be a function of L/R. Being that at slower engine speeds the effect of a short rod on Intake causes few problems. Compression/Power Stroke should produce different emissions than a long rod. Short rod Exhaust Stroke may create more reversion--EGR on a street engine.

3. More exhaust lobe or a earlier exhaust opening may defeat a longer rod. I am saying that a shorter rod allows a earlier exhaust opening. A better exhaust port allows a earlier exhaust opening.

4. Definition of poor exhaust port. Becomes turbulent at lower velocity than a better port. Flow curve will flatten out at a lower lift than a good port. A good exhaust port will tolerate more exhaust lobe and the engine will like it. Presuming the engine has adequate throttle area (so as not to cause more than 1" Hg depression below inlet throttle at peak power); then the better the exhaust port is, the greater the differential between optimum intake lobe duration and exhaust lobe duration will be--ie. exh 10-o or more longer than intake Carbon buildup will be minimal if cyl is dry.

Common rod lengths  
stock length Hemi 6.860
stock length 440/RB 6.768
stock length 400/B  6.358
   
used in stock and +.100 deck height motors
 
(1/8 long )   -   6.985
(3/16 long)   -  7.047
500" low deck motors (stock)    -  6.800   - 6.890