Christine,
The BiG difference between the 94TM and 95TM heads is the head portion of the combustion chamber.
:SINCE YOU HAVE A 98 COMOP::
-If you are using 95TM, then don't use SOHC flat tops, mill the heads to achieve desired compression (0.03" will yields about 1 point).
-If you use 94TM heads, then SOHC flat tops are perfect for a point of compression.
In regards to correct push rod length you simply need to make the choice to use it or have a less efficient valve train (PERIOD). Smith Brother's website is easy to Google. They offer several solutions to help determine the correct push rod length for YOUR engine.
From what I've experienced the stockers were probably OK for the 1st 30k-45k, after that the 4.0L ohv was due for a talve train adjustment but since it was designed without that feature, it's reduced performance is eminent. It all books down to lifter preload.
In regards to needing a different length push rod with a replacement cam, they are a number of factors; increased lift, stronger springs, reground shafts...
In summary, the prudent move with a 4.0L ohv rebuild is to actually measure the required length, then decide wether YOU want to use that for 30-45k before needing longer push rods, over and over and over, OR, get a custom set of adjustable push rods which will insure the highest possible performance eficeincy for the longest possible term.
There us nothing wrong with using stock piston rods but get ARP connecting rod bolts. If you want to get some more power back from the enginerrs at Ford, there are 3 types used in this engine; the set marked "F boca" (known as the RIBBED style) are the lightest and offer a rotational wright load reduction to the engine = increase in efficeintcy.
Two other considerations with the connecting rods are:
1) peening, having stock rods peened will increase their strength and is much cheaper than buying forged.
2) annealing, having stock rods anealed will also increase their strength and is alsi much cheaper than buying forged
Both processed permit the use of stock rids with increased reliability bar the cost of forged rods.