There has been an excellent discussion of the effects the changes to the pikeman would have.
I really agree with Bestbrian, if you want to make the pikeman the most used unit in middle ages, then you need to give it such bonuses that it will become the centre stack defender. This can be done in an excellent way by making them like landsknechts: 6

+100% against mounted and melee.
This will make them slightly better than macemen in a one-on-one battle (9 vs 8). It will make them better than knights in a one-on-one battle (12 vs 10) and thus you'll want them in your stacks. And this is historically correct for the late middle ages. They are still weak vs the fortified longbowman and the crossbowman which is also historically correct since their ability to keep units at range is of no use against bowmen while they will suffer against these units because of lack of armor.
Macemen will still be the primary city attackers although you could consider removing the option of city raider promotions from the pikemen. They shouldn't be decent at city attacking. Knights are there as the dumb brute force attack units.
Crossbowmen are there to make sure that pikemen will have a weakness. They can easily defeat pikemen. However, I think giving them the ability to target melee units first outside cities is not a good idea. There is no contemporary melee unit that can stand up to them, so they'd generally win on the attack which circumvents Civ4's stack defence system. I think it would easily overpower crossbowmen to the point where you don't want melee units in your stacks anymore.
So without the special targeting of the crossbowman, I think this would really work and be more like late medieval combat.
However cost wise, I think some differences should be made. The crossbowman is generally less useful than the pikeman, it's mainly a counter unit. The pikeman is good vs melee units and mounted units while the crossbowman is just good against melee units. The macemen is also more important as it is good vs cities. So I would make the maceman and the pikeman 70

while the crossbowman could be 60
I would like to remark that similar changes to the spearman could also be defended. Their current weakness against axemen and swordsmen doesn't really represent the historically excellent ability of the spearmen in phalanx formation which could fight against the best melee units.
How about this:
axemen: 5

25% bonus vs swordsmen, 35

spearmen: 4

100% bonus vs mounted, 25% bonus vs melee, 25% bonus vs axemen , no city raider promotions available 35

swordsmen: 6 strength 45
This would make the organized spearmen formation the counter against unorganized wild melee units like the axeman. It would make axemen the counter against swordsmen. Finally, swordsmen with their higher mobility could beat the rigid spearmen formation and would be the primary city attackers. Before swordsmen, the axeman would be a better city attacker than the spearman, but the spearman could beat it in the field. It would be fairly accurate historically and would be good gameplay. It would also make the spearmen a far more important unit in the ancient/classical age.
As you might remember, I'm pretty much in favour of reducing the damage that siege units do. It would improve their survivability while making the job of taking the city harder for the other units. It would result in lower losses amongst the siege units and higher losses amongst the other units. It would also not make the battles after the siege units have attacked trivial.
However, I can imagine that you have a different idea for your mod so you can just ignore my rambling in the above paragraph.
However, a different issue. I just downloaded this mod and was checking out how ranged bombardment worked. I wanted the know how well balanced it was compared to normal attacking. What I noticed was not really expected:
Siege units that can do ranged bombard can kill units with ranged bombard while they cannot do this with a normal attack. That seemed weird to me as they risk far more with a normal attack than with a ranged attack. Shouldn't the ranged attack have a similar damage cap as the direct attack or maybe even a higher damage cap (you can do more damage in a risky direct attack than with a ranged attack).
Example: the artillery has a normal damage cap of 85. It cannot reduce units below 15 hitpoints with a direct attack. However, it can kill units with ranged bombardment. Wouldn't it be more balanced if ranged bombardment would have a higher damage cap (like 50 hitpoints?)
Note that ship ranged bombardment can also kill.